How I Would Rewrite the Mass Effect Trilogy to End Better
The real weak point of the Mass Effect trilogy, I think, is the second game.
Why?
It is largely because the game's plot is split in two. The minor loyalty plots are character-centric and-- with the possible exception of WTF of Jacob's-- interesting and emotional. They tell stories you want to hear, about people you want to know better.
The big Collector plot is so simplistic and on-rails that it's not terribly engaging. Somehow, there isn't a lot of emotional connection, even where there should be, i.e. the Prothean reveal and the loss of the colonists. I got more feeling out of the Prothean reveal chatting with Mordin about it than I did on the (I think the three?) Collector-centric missions. There wasn't any staying power to that emotion, either. The colonists were kind of the most 'FEEL SAD, DAMN IT!' thing in the entire series, worse than the kid in ME3. You just learn too late what exactly is happening to them, and then you meet the baby Reaper and wonder why a monster from Power Rangers showed up. It all lacks a sense of impending doom that you got from the first and third games.
The main plot is designed to be leisurely, in a sense. You can't sacrifice that without destroying player freedom and the good elements of the story. What was good in this trilogy, and there is a pretty decent amount of it, was really good. The main plot needs to be more interesting, which would make it seem more urgent as well.
First thing's first. The Collectors need to be more engaging, on many different levels. They were truthfully rather boring in combat, which I suspect might be the reason you never fought them in ME3 but did face down Geth and mercs (or Cerberus, same difference) in all three games. The ME3 Codex states that the Reapers are still using them, so it's not like they're all dead. They need to be more fun and unique to shoot at. They weren't. The ME3 enemies, on the other hand, were.
Also, they need to be engaging as a species. That they weren't makes some sense; the Collectors are less of a race than the Geth ever were, mindless slaves without culture or thought. This works very well in writing, but an interactive and visual medium needs something more personally engaging. Harbinger lacked, because it was a truly faceless, ranting villain without anything interesting going on.
Solve this by making the Collector General a real character, not a reference in the codex and a cutscene. Let it be the last struggling Prothean, bound to Harbinger's will but fighting in what small ways it can to help you. This fits, I think, with the 'victorious defeated' theme the Protheans have had since Illos to Thessia to Javik. We've seen people fight indoctrination (Benezia, Saren) enough to do something useful. Let it be in a subtle war with Harbinger for control. It loses in the end, heartrendingly before you, but what it did to help you mattered. This would reveal more about Harbinger, too, I think.
What should it help you with? This is where things really change the plot of the series. It should help reveal more about the Reapers, their origins, and their motives. Not a ton, not perfectly clear answers. The main plot should still be humans being taken. Maybe it sends the Collectors to colonies where info has been/ can be found, leading you into some ancient ruin or some battered console. The Reapers don't like things known about them, that's clear in ME3, so there must be a weakness in there somewhere. Hints at the catalyst, hints at their motives. The rest of two precedes apace, but the game seems to hold more overarching meaning. Also, redesign the Reaper larva. That creepy conceptual fetus design would have worked very well.
Now, the Reaper's motives. Apparently, the original version had it be a 'save you from ourselves' thing involving mass effect technology use increasing the entropy force (dark energy) of the universe. There were hints, and it's certainly space opera-ish, but I think it's a stupid reason and lacks a thematic and plot fit. Why did the Reapers leave the mass relays, then, if they caused the universe killing problem? Sovereign outright states that they made sure organics would end up using this tech, that they wanted them to. And why the tortuous death instead of straight up orbital bombardment everywhere with strike teams to clean up? EDI tells you a story from the Holocaust put into Reaper context. They want to destroy people's spirits, not just their civilizations. Why bother?
The Reaper's motives make more sense as something ideological/religious than something practical. It explains the torture and the arrogance.
Mass Effect has had one very clear theme across the board: if we work together, we can beat them. The rifts we see between the various species, and even the internal rifts, are exploited by the Reapers for our destruction. These conflicts are the source of a lot of pain and horror in the galaxy. They're also inevitable, a part of living things (even synthetic). Shepard can mend a lot of bridges, but not all of them. And, truth be told, sometimes the price isn't worth it (you heard me, dalatrass. I don't give into your amoral whining).
"We impose order on the chaos of organic evolution" Sovereign states. The Reapers are a force for order. They are vast hiveminds. In my rewrite idea, they believe that organic life is so rife with conflict that is fundamentally offensive. It must be destroyed. Their origin? The first Reapers were an organic race that desired order, and created the Reapers to become gods of order.
So why not simply kill all organics? Because from time to time, a race rises that they believe is worthy of joining them (possibly all races; the ME3 codex is nebulous on this point, now). They consider this, as well as the end to chaos, their sacred duty ("We are your salvation through destruction"). They allow young races time to progress along the set path and see where they go. They don't mind floating in the void, because what is more orderly than the nothingness?
The Catalyst figures into this as the 'regulator' of the cycle, a high priest sort of thing.
With this in mind, and the hints woven throughout the trilogy, when you meet the Catalyst, you are given an argument on its ideology. A good argument, actually. If organic life is doomed to chaos by nature (and all clues point to the fact that it is), shouldn't there be a regulatory force of order? The only thing that unified these fighting species was the outside threat, after all, and they will likely war again if they live. Nothing will be truly preserved without the Reapers.
With the Crucible, however, you have the winning hand. You can direct (not control) the Reapers, and the Catalyst is utterly helpless. The Illusive Man needs to be wrong, I think. It fits with the Cerberus theme of general abject failure and completely mistaken assumptions.
You can send the Reapers out to dark space, where they will wait another 50,000 years, then return to bring order to a no doubt warring galaxy, where all you cherished will no doubt have been reduced to dust by conflict, utterly forgotten. Or you can destroy the Reapers (and just the Reapers), leaving organic civilization to live and roil in its natural chaos with no one to bring order. It may even wipe itself out, in time.
This is very paragon/renegade, though I suppose which is which is a matter of interpretation. I know mine. It leaves your actions to matter and gives the player a chance to explore this universe in future games. Galactic civilization is not utterly destroyed as int he current endings.
Whatever you choose, your war assets determine the course of the battle below, if Earth is left as anything more than a dessicated husk of a planet by the reapers parting blow. I think War Assets were a good addition to the game, personally, and that gives them some impact that makes sense.
Also, Shepard bleeds out after the choice is made. I don't think Shepard's personal story was ever supposed to end well, but then, my LI inevitably died in ME3 (wouldn't change that, actually, except make it not in a hospital). I guess War Assets could determine this, but I have dramatic visions of Citadel go boom and it makes no sense.
Oh, and the Normandy lands on Earth-- utterly or just mostly devastated depending-- and your surviving crew and party members, past (if Earth won) and present, make an appearance. And then DA style notecards during the credits with pretty music.