Considering the fact that research on concepts such as
Organic Computers is going on now, I'd say a race of machines millions of years old could reasonably use the genetic material of a species to make up a sentient starship.
The most common complaints I hear in reference to the Reaper are that:
1. It wasn't explained well enough. While this may be true, if they spelled out exactly what the reaper was being made for(let's say it was another Sovvie) then we'd be upset that they don't think we're smart enough to infer that on our own. As for how it was being made, it's technology millions of years more advanced then ours, that's essentially freaking magic! Even if we assume that it's only a few hundred years ahead, that's still more then advanced enough to make it damn near impossible to explain. Could you explain a computer, or a solar panel to someone in the 18th century and expect them to understand flawlessly? Hell if you went back a few decades and proposed CPR or a defibrillator then you'd be locked the hell up.
2. Why did it look like a human? This doesn't really have an explanation, if you want one then you could potentially argue that it would on some unexplainable level make it a more pure essence of Human culture. If they really are "arks" of races that came before then it would serve to preserve the soul of the species. As for why it didn't look like a fetus... Well honestly that would have made even less sense. How would it grow then? They'd break apart links and reweld every few weeks? No. In addition, that thing was no where near the 2km that Sovvie was, it was maybe 300-400 meters tall, that's less then a fifth of the final design.
My point is, this is way too much scrutiny and emphasis on something they already know people didn't get. Reviews said it, hell almost every review said it. THEY KNOW, you can now move on to complaining about the other 50 or so minor things that no one outside these forums let ruin the game for them so that Bioware knows that it wasn't ideal.