The only reason Shepard was against controlling the Reapers was because he thought it was impossible, since Illusive Man was cruel and indoctrinated
But then he finds out he was right about them being able to be controlled.
The ending doesn't kill off synthetics, nor does it forcibly rewrite everyone's DNA. Shepard uses the Reapers to improve everyone's lives. Don't see what's so wrong about this, besides Shepard becoming a computer basically. That's the only bad thing for the galaxy at least.
Possible reasons people could call the blue "control" ending wrong:
1) There's the speculation that Shepard will become corrupt with power and enslave organics to serve the machines. Personally, I don't think this is possible, it's not like Shepard's mind is still actively controlling all the Reapers individually; I saw the control ending as Shepard rewriting the Catalyst's chief objective from "Preserve organic life no matter what" which lead to the cycles and changing it to "Assist living species without harming them", which will not lead to the cycles or to enslavement. I don't think Shepard is still "thinking", I don't think this protocol could change until someone else fired the Crucible.
2) There's the idea that Shepard was indocrinated all along and will not change the old Catalyst's ways too much for too long, that the ending was mostly some sort of Reaper-influenced dream sequence. Myself? I disagree, I think Shepard was still Shepard when he/she made the decision.
3) There's also those who disagree with it because of what it does to EDi and the Geth - they finally became self-aware individuals, capable of learning and falling in love, and Shepard gets rid of all that instantly. To many, that is a bad thing for the galaxy. Personally though, I think it's worth it: I think I speak for EDi and Legion when I say that if I had to give up my mind and personality, if it was for Shepard I would.