I just personally think Control is the worst ending.

You're basically doing what Starchild McSpaceMagic did in the beginning. Weren't the Reapers there to preserve life when they were first created, not eradicate it to make more of it's kind using the genetic slush of the most superior species of that cycle? I'm not going to question the strength of Shepard's will, but it's inevitable that he'll eventually come to some kind of wacked out conclusion as the Reapers had. And then you have mass genocide again because the Shepard-Reapers fell back into their 'no one can be trusted with their own lives' god-complex assholery.

I went with Destroy in my first run through, but thinking back on it, I may choose Synthesis over it if I were to go through the game again. I mean, to be honest, you're either going to have to commit genocide, potentially come back to destroy the entire universe... again, or you just have to play god to make a race of possibly perfect beings without their consent. Hard choices, but I'd say the latter is the best.