Ok, here is my understanding. We knew from the last game that Reapers allow organic civilization to reach a certain point and then Harvest it. But for what? They don't need the technology, and they didn't keep the slaves.

The reveal here was that each Reaper is in fact the genetic sum of the species that came before... they are harvested and distilled into Reapers, somehow possessing not only the genetic markers of that species, but their group consciousness, somehow. The human-reaper was not designed, it grew based on the genetic material that was being fed into it. This, in short, is the Reapers Reproductive cycle. So a Reaper made of Turians would look Turian, etc. The choice of Human can probably be laid at Shepherd's feet... if Humanity is capable of destroying a Reaper, then clearly they are "worthy" to be made into a Reaper themselves.

I agree that the boss fight was a let down, though. Maybe I need to ratchet up the difficulty, but I figure even an embryonic Reaper should have been a bit tougher to handle. Of course, being Embryonic, if it was tougher to fight that Saren/Sovereign...

Story wise, I liked it. Gameplay wise, I could deal with it. It is the middle installment of the trilogy, after all.

Did that help?