These are going to be brief notes rather than an actual argument, largely because my brain is still broken from watching all of FMA and from the beginning episodes of Princess Tutu.
Disclaimer and standard grain of salt: My understanding of shounen tropes is taken from sports anime/manga, fighting anime/manga, and some mecha anime, though most of the tropes that I'm used to come largely from the arena of fighting anime/manga. Also, my samples pretty much consist of Bleach, Naruto, Hikaru no Go and Kenshin. I also don't read/watch that much shounen, so again... grain of salt.
Also, I generalize a ton with regard to shoujo and shounen; I don't mean to imply that female equates emotion while male equates physical. I'm being more descriptive than prescriptive in terms of the genres, given what's largely out there in the market.
Spoilers for all of FMA
1. Dangerous Sekrit Techniques that Usually Aren't All That Bad
I love that the anime opens with what would normally be the gleaming moment of triumph in most shounen series -- the heroes, incredibly talented for their young age, are defying the rules, and for the most part, it looks like they're succeeding. We get shots of Ed and Al's triumph and joyful faces as they master the most difficult thing in alchemy.
And then things go really, really wrong.
I feel like in a lot of shounen, the heroes go off and do things that they Aren't Supposed to Do. Normally, these things are usually things that have consequences only for the heroes, such as assorted dangerous jutsu that the ninja in Naruto should never use, for fear of death/losing their powers/going over to the dark side/whatnot. Same goes for Ichigo and his assorted power ups. I think these moments usually come in the middle of series, during giant fights of doom and pain, when the heroes must pull out that special secret or lose anyway. The narrative usually puts them in a position in which it's a heroic choice, and they make it knowing the consequences to themselves, but never really put anyone else in danger. And usually, after the dreaded secret fight technique is pulled out, the hero suffers some consequences, but never any permanent ones that will disable him.
Ed and Al, are, of course, doing this for their own personal gain, not for the good of others or to protect their precious village/friends/family/loved ones. And while the consequences are personal and very painful, the big thing is that Al bears the brunt of it, whereas it was Ed's idea to attempt human transmutation. And then, there's that horrifying image of their mother. Finally, it's a huge consequence to pay; while usually shounen heroes lose some ability for a while, they eventually recover it in the end. The shots of Ed's missing limbs and Al's disintegration are pretty awful and permanent.
And the best part is, that's how the series begins; not with a moment of triumph, but with horror and the best intentions gone awfully wrong. This is in contrast to most shounen series, which start out with the young hero discovering his burgeoning powers, be it in go or ninjutsu or basketball. Ed and Al begin with something being taken away; worst of all, it's not being taken away because of someone's else's villainy, it's being taken away because they made a very bad mistake.
2. Very Precious People
A LOT of the anime and manga I've seen and read involves the protection of some Very Important Person to the hero or the heroine; one of the distinguishing factors between shoujo and shounen is that the shoujo heroine protects emotionally by becoming more gentle and caring, while the shounen hero protects physically by growing stronger and mastering more and more battle techniques. I suspect this is more for shounen subgenre of fighting manga/anime, as opposed to sports, in which the emphasis is most just on growing stronger instead of on protecting aforementioned Very Important Person.
We basically get from the beginning that Al is Ed's Very Important Person. Ed is also Al's Very Important Person, but generally I feel that is downplayed a little bit more, though still important, just because Ed is the big brother and feels most at fault for what happened. And Al lost his body, while Ed lost two limbs (very sucky, but not quite as sucky as living in a suit of armor). Ed's also set up as the standard shounen hero because he is Speshul -- he can do alchemy without drawing a transmutation circle, he is the youngest State Alchemist EvAr (I think), he passes an examination that very few people pass, and of course, there's the fact that he's called the Fullmetal Alchemist.
And of course, because this is shounen, Ed will do anything for his Very Important Person. However, while this is usually portrayed as a good and noble thing, here it's a deeply ambiguous thing at best. Ed becomes a State Alchemist for Al, looks for the philosopher's stone for Al, both things that cause Ed to do some things that he would probably rather not, and the latter being particularly calamitous. Also, while shounen heroes usually do have some failure to protect a Very Important Person in the past, causing much trauma and an even stronger desire to protect their current Very Important People, usually that failure is drawn as being more in the hero's mind than anything else (aka, it is angsty because the hero thinks it's his fault, but anyone with a brain can see that it was really the fault of the monster that ate his mother/brother/family etc.). Ed, on the other hand, is fully culpable, and the series in fact opens on the act that makes him culpable.
Anyway, back to my point. Ed's actions to help Al could very well be played off as heroic and self-sacrificing, and it is, in a certain context. Unfortunately, that's only in the Elric's world, and doesn't include the world around them. For the world around them, Ed's quest to restore Al's body is a very dangerous one; even when he's doing good as a State Alchemist, he wreaks havoc (see: Liore), and the quest for the Philosopher's Stone is ultimately one that forces Ed to weight Al's life against other people's.
The same things happen with Al as well, even though he ostensibly doesn't make as many sacrifices as Ed and isn't quite as single-minded as Ed is in the beginning. But when he's confronted with Wrath, he's the one who goes berserk and tries to cut off Wrath's limbs to return them to Ed.
I really like how the series deconstructs the idea of protecting your Precious Person, particularly the notion that just attempting to protect your Precious Person is enough to make the world a better place. I mean, you get the notion of protecting a Precious Person as being essential to making the world better in Naruto and in X (to throw some shoujo in), even though Naruto does emphasize that a village or a world can also be a Precious Person. But I think FMA goes the furthest in showing the effects of protecting your Precious Person above other things, and whenever Ed and Al make the choice to do so and disregard things like the laws of alchemy or the effects on other people, things go wrong.
And to decentralize it, the protection thing isn't just critiqued with the brothers. People who try to protect the brothers often end up failing as well, particularly when said protection involves the concealment of information. But that goes into something else all together, which hopefully
fmanalyst will finish
writing up. In the end, wanting to protect your Precious Person will not alleviate the consequences of your actions. I particularly liked this because there are so many series (shounen and shoujo, anime and Western) in which a person clings to their Precious Person(s) (see: Buffy) and that is somehow never contradictory with their attempts to protect the world as a whole.
3. Speshul Abilities
This isn't limited to shounen (see: magical girls). Ed is Sooper Speshul in that he can do alchemy without a transmutation circle.
This is actually going to be a minor point, but this is the thing that actually had me grinning because it was so a deconstruction of all those shounen series.
One of my very favoritest things about FMA is that there is an actual reason why Ed is special and that other people can be special too. It's not like Ichigo miraculously being able to wield the largest zanpakutou EVER or Naruto having the power of the kyuubi in him or even the hero of Yakitatte! Japan having the "hands of the sun" (I kid you not. Go read it, by the way, it's a sports shounen manga on making bread and it is hilarious). Granted, Naruto is much better at downplaying the super specialness of its hero and showing his shortcomings, and it's better at showing how different people are special at different things, or how determination and hard work also make up for a lot. But there's that element of chakra control and etc. still.
When FMA starts, I just assumed that Ed was magically talented as an alchemist, either because of his alchemist father or just because he was the hero of the show, if you're reading the show as standard shounen. But then there comes the Big Reveal about the Gate and how Izumi can do alchemy without a transmutation either! And the best thing about this is that the hero's specialness isn't actually specialness, it's a consequence of attempting human transmutation, which is never, ever, ever a good thing.
4. Fight scenes
FMA obviously isn't standard shounen because it doesn't revolve around fight scenes/battle scenes/sports competitions. I mean, aside from all the reasons above. But I really like what they do with the fight scenes.
Now I am reaching the part I didn't think about so much, so this is going to be a lot shorter.
But there's remarkably little one-on-one fighting in FMA, while that seems to be the standard format of a lot of shounen. The ones that I really remember that involve Ed and/or Al are the fight scenes with the live pieces of armor at the 5th lab, Ed's duel with Roy, Ed's fight with Greed, and ... Ed's fight with Barry the Chopper? There are amazingly few duels with Scar, and the other notable one I can remember is Roy vs. Pride in the very end. I suppose you could count Ed vs. Envy in as well.
I think a lot of shounen uses the one-on-one fights as a means to make their characters grow. If it's done well, it becomes character development (yay, Naruto!). If not, usually it's just a character's chance to learn a new technique and/or come back from the edge of defeat. But the big thing is that the characters gain strength from the battles and learn that they, too, can protect their precious people, help save the world, protect their village, bake really good bread, etc. It brings them closer to their ultimate goal. I can't really remember that many of Al's fights, but Ed's one-on-one fights almost always end poorly for him (I think). He usually ends up triumphing, but in a way that breaks him emotionally, a la the Barry the Chopper fight.
Hrm, I think his opening fight with Cornello is the most standard shounen-type fight in the series.
Anyway. Ed's fight with Greed again ends with Ed triumphing, but he's obviously broken up about it. I will say that a lot of shounen one-on-one fights end up with the hero having a bittersweet victory, particularly when it's against a Big Bad and the Big Bad eventually regrets his actions or reveals his tragic background, but there usually isn't the disillusionment with fighting itself that comes from some of Ed's wins.
I think Roy's fight with Pride is a more standard shounen fight as well.
I can't think of many with Al, just because Al is so notably the not-so-violent one of the pair.
5. Violence and war in FMA
Another thing that I really like about FMA is that it really shows how much damage war and violence does. I realize that I am very much stating the obvious. But really, lots of shounen tends to decry war and violence but still glorify the individual fights/using violence for self-growth. Everyone always seems to talk about wanting to not have to fight to protect people, but the fight scenes are done with such glee that it's hard not to like them.
Plus, in these things, the hero's ability to do ninjutsu/execute Hollows/pilot mechas/swordfight is seen as a good and cool thing. It's often complicated by the hero's Dark and Tragic Past in which he did not protect his Prior Precious Person, but since the hero's Dark and Tragic Past usually isn't quite as Dark and Tragic as he may feel, said angst about his [insert martial ability here] isn't quite as immediate to the viewer. And there's a whole bunch of cool vocabulary and paraphernelia that tend to go along with said martial ability, from weapon power-ups to different ninjutsu or just better and shinier mecha.
First off, FMA has some really brutal fight sequences that just leave you cringing, and it takes a really hard look at military prowess as a whole. Then, Ed and Al never really get cool power-ups or paraphernelia; in fact, the one bit of paraphernelia that they're looking for is incredibly destructive and everyone searching for that bit of paraphernelia has basically wreaked havoc and woe everywhere they went. I think one of the reasons why FMA is rather lacking in the one-on-one fight sequences is because it focuses on organized fight and war. There aren't that many duels, because duels are impractical (why in the world don't the eighteen other minions ever rush in and attack en masse?). Instead, there's the military overpowering civilians, a whole military-alchemical complex and etc.
But I think most shounen series tend to portray mass violent action as bad -- the difference is that that violence is often displaced into individual duels. FMA doesn't shy away from the fact that not only is there mass violence being committed against people, but also that the Elric brothers are complicit in that mass violence. It's not just Ed being a State Alchemist and a dog of the military, it's that end reveal that their quest for the Philosopher's Stone is the thing that actually drives the homunculi and Dante to stir up wars. Even though Ed and Al don't know that from the start, that doesn't stop them from being culpable.
And back to paraphernelia and power-ups. Another thing that I love about the series is that any attempt to get a power up is basically a very bad idea. All the alchemist are basically trying to get power-ups by chasing after red water and the Philosopher's Stone, and really, the attempts to do so are posited as an attempt to go beyond the fundamental rule of alchemy. Other attempts to go beyond the rules of alchemy or to do things that other alchemists have never been able to do are always bad things, and the one power-up that Al gets is something that results from the death of thousands and thousands of people. Contrast this to the ever increasing personal power of the ninja in Naruto or the shinigami in Bleach. Usually in a shounen series, the protagonist believes that if they only train hard enough and work hard enough, they too will be rewarded with that power up (and if they are sooper speshul, they can get to it really fast). In FMA, it just doesn't work that way. There is no power-up to be gotten from alchemy.
The one real power-up in the series is arguably Ed's final act of human transmutation, which brings Al back from the dead/the Gate and restores his body, but instead of coming from hard work and training, it's an unselfish act of love that still has some pretty painful consequences. Arguably, Ed's realization that equivalent exchange doesn't work as a moral perogative is a bit like the realization that training hard enough and working hard enough still won't get you your reward. Like Roy says to Ed in the end, sometimes you do what you do even though you know you won't get rewarded.
Which now brings me to the rambling thought that the philosophy in shounen series may be a sort of equivalent exchange -- work hard enough, try hard enough, train hard enough, and you, too, can be a hero or a star tennis player or a kickass ninja. FMA says instead that you can do that, but it still might not happen.
Anyway, I am running out of bullet points.
In conclusion, go watch Fullmetal Alchemist!