Okay. I've watched THE WHOLE SERIES. Which I felt was the fair thing to do since DS9 takes a while to get rolling too, and honestly if you drop out of DS9 before the last episode you DO miss out on fairly big plot points.
Babylon 5
Pros:
* Equality of women and (in general) non-white cast. I list this first because it is, frankly, something that impressed me quite a bit. There is much more representation of women and not-white people in the general cast of the show than I was expecting from something out of the 90s. Granted, a lot of the recurring female cast members wound up with character-altering relationships, but on the whole the show's willingness to cast women in positions of authority (and just cast them everywhere, so that you had a near 50/50 of a new character being female the way it's supposed to be) was really nice. The representation of minorities isn't as good, but they seem to at least have been trying.
* Consistency of arc. For this one I am glad I waited until having seen the ENTIRE series because until I did there was a fuck lot that looked from the front end like filler or just a joke, but while I do not agree at all points that the showrunners had a GOOD story to tell, it is fairly clear when viewing the series as a whole that they did in fact HAVE a story to tell, from the getgo, and more or less spent the whole series telling the story.
* Not Quite Planet of Hats. The cultures on this show did get some fleshing out, mainly through more than one recurring actor playing each race. So you got to see Centauri arguing with other Centauri, Narn arguing with other Narn, and Minbari arguing with other Minbari, which let each culture get a bit of breadth and depth.
Cons:
* Theft of not just story plots but really well known story plots. When I'm looking at several episodes and thinking "did no one in this universe read 1984/Lord of the Rings" that's just way too blatant a theft going on.
* Story driven by Stupid. No, really. In several places the story only works if you assume that everyone in the known universe has a brain the size of a small garden pea, and therefore can't tell when something is in or against their best interests. Now, I grant you, there's a lot of Stupid in the universe and most of it winds up in government somehow, but this show really pushed the boundaries of Really Fucking Stupid.
* A complete lack of grip on current events. This one really, really bothers me. As far as I can tell, there were at least three wars during the five seasons, but I couldn't tell you for sure when any of them started, or ended, or what kind of toll (if any) they took on Babylon 5 or her staff. The reason for this is that every single war was going on in the background. It was hugely rare for any sign of attack, or wounded, or seeing people fly off to battle, or even much in the way of battle reports. This tended on the whole to mean I neither knew much about those wars, nor cared much, because they clearly didn't matter much.
Deep Space 9
Pros:
* A much longer and more depth filled arc. Part of this is that DS9 got seven seasons where B5 only got five, but since DS9 took a few seasons to get going, in fairness it's really more five against five. And in this, I will say DS9 on the whole had much better storytelling. There's a lot more gray, a lot more fear, in the episodes. And while Sisko, like Sheridan, is a Messianic figure in his show's overall arc, Sisko remains a lot less mystic and more down to earth even when he spends an entire episode hallucinating. And Sisko's farewell is no gentle goodnight; he goes down fighting.
* Much better STORY. Oh my god. When the Maquis arc hits, it hits DS9 directly and repeatedly. When the Dominion War hits, it hits DS9 directly and repeatedly. DS9 is not separate from the action, it's right in the middle of it. The wars and conflicts affect the station and its personnel directly throughout the duration of those conflicts, which is what makes them matter to the viewer.
* While the one shots and extras tend to be white men, where DS9 puts gender and race in the front, it means it. Sisko is very likely their best captain in the entire Star Trek universe, because while he is a Captain first (as one should be to GET the job), the fact that he is a black man is not negated, ignored, or made to alter the role of Captain. In this show at least Star Trek got casting a not-white-male exactly right. For an example of how NOT to do it, see Voyager.
Cons:
* Much less representation of women and minorities. They try to counter this by giving the women that ARE regulars positions of power, and character development, but when contrasted against B5 the net result is DS9 is set in a blandly white-male universe against which the main cast sparkles in color, where B5 used the full spectrum foreground and back. The exceptions being noted in the pros section.
* While we're on the subject, there's some serious issues of Not Okay behavior, especially by Bashir in the early seasons. He is, frankly, a stalker. It is not cool. He should've caught some kind of consequence for that.
* Inconsistency in early seasons. You can really tell, early on, that the showrunners weren't entirely sure what to do with this 'set on a space station' idea. There's some character development, some expansion of the Trekverse, but as to story and arc, it's pretty uneven. The best that can be said for it is it does tend to factor later on...but that's it.
Conclusion:
I'm definitely a Niner, and probably always will be, but that doesn't mean I think Babylon 5 sucks. There's some preferential issues in play here - I prefer solid storytelling, which DS9 has much more than B5. And I'll take a solid story over solid character, which is where B5 is strongest. (I will happily concede that Londo, G'Kar, Ivanova...everyone but Sheridan and Sinclair really got some beautiful and in-depth characterization. The problem was mostly that the stories these characters were used to TELL didn't interest me.)
Both DS9 and B5 have messianic arcs and this is, frankly, a negative to both shows. The reason I then prefer DS9's to B5's is DS9's is explained. Fully. Why it's Sisko and not some other guy. Who's choosing him and what for and why they had to choose ANYBODY. And, most importantly, while there is no actual mysticism to any of it, the show is fairly clear about where a mystical interpretation would come from. In B5, there's just "and then there are these really old races who can do shit so far past us we gave up and said it's magic". I had to ask - WHY Sheridan. WHY Sinclair. Was it just that they happened to be in the right place at the right time? It kind of seemed so. In B5 you're just...forced to accept the giants in the playground, as they put it. With DS9, questioning ANYTHING that calls itself a god is taken not merely as a given but as a solid responsibility, and more than one episode is based around figuring out WHY shit that looks 'magical' is happening.
In my ideal happy show, you'd have the optimism and 'explain the mysticism' of DS9, the storytelling of DS9 and the characters and races of B5.
And I say the optimism because while DS9 is easily the darkest of any Trek show, it's several notable shades lighter than Babylon 5, where entire races die out of Stupid. And frankly, I don't need my entertainment to be THAT dark.