Introduction: The ending was a cop out/cheesy/a rip off/stupid/terminator/one-word-answer-with-no-actual-argument-as-to-the-good-and-bad-points.
These are the majority of the arguments I've read about ME2's ending and Bioware's decision for the final boss. Again I would like to try and have intellectual arguments about what is and is not good about the resolution of the game. So, what I can gather, the only logical argument is that they haven't explained exactly how grey goo => Human Reaper. Fine, I'm not sure, exactly, if they explain it well or not, or if they will ever explain it. However, I would like to bring attention to a few things. Before I get to the how and why, I'd like to start with the "what."
What the Game Tells us Specifically:
From ME1, we know, at least at some level, the Reapers are a "nation" as well as an individual, insofar as they're not exactly like the Geth. The Geth are collectives, they are the Geth, all and one. The Reapers, however, even have names for one another, suggesting they're somewhat an individual, at least somewhat so. The Reapers, also, are a mix between Organic and Synthetic parts. This is also revealed in the game. When we go into the Derelict Reaper, they mention Nanobots, do they not? Now, I've heard many a time the "grey goo" described as what we would see if there were a large clump of nanotechnology grouped together. This all leads me to the following speculation.
The Reapers supply the Collectors with far advanced technology. We aren't even at the level of the Protheans and they had created a mini mass relay, suggesting that perhaps the Reapers might get some technology from the Protheans even, if only a little bit. Honestly, that's how technology works right? You make a big cell phone and now the cell phones are ridiculously small. I'm not saying this is a fact at all. That's really beside the point. What if, the Collectors are using Nanobots to deconstruct humans into more nanobots, which then reconstruct themselves as a Reaper, and the reason that Reaper is in that form is because it is the easiest form for the nanobots created from a human to reconfigure themselves into?
The Reapers are actually a group of consciousnesses aren't they? The collective-consciousness is the "level of existence" that we cannot comprehend right? Because their we have A.I. capabilities in this world, it isn't too far of a stretch to say that human consciousness can be downloaded into a program. Perhaps the reason they need Humans alive, i.e. the reason they use stasis bugs instead of killing everyone and using that genetic material, is because the hundreds of thousands of humans that go into the reaper keep their consciousness on some level. They need the humans alive and conscious, something I'm not sure can be built into a clone, at least not the same kind of consciousness.
I do not claim to know much about nanotechnology. I'm a Psychology/Philosophy double major, I'm not exactly a scientist. However, I do like to think I pick up on cues the game gives me, and that I like to think about those cues. I think that this makes perfect sense in the design of the plot. The end game boss, then, shows us very much. What the collectors are doing, how reapers are created, why the reapers use Sapient life to create those Reapers, and throughout the plot the game shows us what happened to the Protheans. This, as far as I can recall, is a lot for a sequel to show in a Trilogy.
Yes much of the game is recruiting characters, which may be rendered useless if you get a new cast in ME3, I say we wait to complain about this until then however. It does make up a majority of the game, but that gives you a game to play, to get to know these characters, to see into their background, with time in ME3 to get to know their characters a bit better, as we did not delve into every aspect of each person's character quite obviously. I cannot think of a better way to give us a big game that shows us a lot about the main story, in a dramatic way, without dragging out the finding out of actual usable information. If you don't care about certain characters, the game also allows you to discontinue the impact of those characters. Overall, I think the game is very well done. If you don't care about most characters and just want to see the end of the game, it can be done in under 10 hours, keeping characters you want alive.