I'm just going to post this here for more comments. This is an idea I brought up a while ago but it never got much discussion going for it:
I would like to suggest the possibility that the Reapers are nothing more than very advanced husks, Leviathan husks in particular.
Being constructed from the genetics of other species would make the Reapers different than the conventional husks we see, which retain at least some outward semblance of the species used to create it. The apparent intelligence difference (or rather, flexibility of thinking) also appears much greater in a Reaper than in a husk footsoldier.
But consider this: from our point of view, husks have a far more limited focus. So much of a limited focus that they seem to have lost their former intelligence and could be classified as sophisticated VIs. Some evidence of higher intelligence can be seen in the strategies they use in battles but, in the end, they only have competence within the context of their function.
But the Leviathans were EXTREMELY intelligent. Far beyond where we currently are in the evolutionary curve. A Leviathan husk to us would seem immensely intelligent. However, a Leviathan would likely see a Reaper as nothing more than a crude, mindless imitation, much as we view human husks.
To me, this means that, as crazy as it may seem, the Reapers are actually extremely complicated VIs. Their thinking appears to be genuine AI because of how complex the Leviathans' minds were.
What this means in the context of the ME universe is, quite simply, that unless the Leviathan intelligence itself is destroyed, the threat that the Reapers posed will outlive them. Shepard destroys the Reapers in this cycle but the Intelligence, should it survive, will try to find another way to fulfill this function. How it might evolve its own methods to do this is a complete wild card at this point but it will certainly do whatever it feels it has to to gain control of evolution.
Anyway, just wanted to throw this out here. Might be a possibility for where ME 4 could go. Then again, maybe not. What's everyone think?