I really like a lot of the ideas here (especially DeinonSlayer's ending rewrite). But like MrBtongue, I crave attention and validation, so I'll throw in some half-baked ideas of my own. What if there were just a lot fewer of the cuttlefish, perhaps just enough so that if they were to attack all the homeworlds of the major races, there'd only be enough for 1-2 per world. Instead of having them show up and attack outright, you could have them pull an "I come in peace" maneuver at the beginning of the game; they show up at key star systems and announce that really, they're good guys and Sovereign was just a bad seed. And they made the relays too! How nice of them! Meanwhile, they're indoctrinating as many folks as possible in preparation for the harvest. This would accomplish a number of things:
1. It would pay off the whole "Nobody believes Shepard about the Reapers" arc of the game, which ended up going nowhere. Shepard's goal for much of the game would be to prove that yes, the Reapers are bad guys. How would he or she do this? I don't know; it's late, and I'm tired and lazy.
2. It would force Shepard to spend a significant amount of time fighting indoctrinated forces. That fits with the "War is hell" motif that ME3 is trying to shove down our throats. One of the things that presumably makes war hellish is the fact that you have to kill real people with interests, goals and relationships outside the conflict. Killing a husk or cannibal, by contrast, is a consequence-free act, morally speaking.
3. It could be mined for some religious references to Revelations or some such, with the Reapers playing the role of the beasts, the relays and citadel standing in for the great signs, and indoctrination a stand-in for the worship of the beasts. As far as heavy-handed religious symbolism goes, it's gotta be better than the Garden of Eden.
4. It might enable conventional victory; if there just aren't very many of the darn things, then with the relay network intact, maybe the combined forces of the galaxy would have a chance against them.
5. It relaxes the "race against time" aspect of the plot, which made it a bit implausible for Shepard to be exploring every nook and cranny of the galaxy looking for random stuff or hanging out on the Citadel while the galaxy is tearing itself to pieces. I've heard some people suggest having the bad guys show up only in the second half or last third of the game to alleviate this, but the worry with that is that introducing and then eliminating the Reaper threat in the span of one-half of a game, after foreshadowing that threat for 2 1/2 games, seems rather anti-climactic. Perhaps this proposal can weave neatly between those two horns.
Well, that's it for now. If anyone wants more bad ideas and incompetent Monday morning-quarterbacking, you know where to find me.