Some keep saying they changed into the 'bad' guys in ME 3. They were always the 'bad guys'. Everything in the first two games was just building to this apex. They were consistently looking for ways to create and control super-soldiers. Everything they ever did was to grab more power for themselves, right up to the end when they wanted to control the reapers themselves for the power it could give them.
And they weren't wrong. Illusive Man was obviously right from the very beginning, Reapers can be controlled. And Control ending is in every way superior to Destroy ending.
So he was right all along.
What completely ruined it, was his Indoctrination. It just didn't make sense, because TIM was far too clever to not take every precaution against that. He was well aware of capabilities of the Reapers. The ending (if they wanted to go with different colors and "Deus Ex" switches) should have been the argument between Shepard and Illusive Man as to what option should they choose (Control or Destroy).
It was such a wasted opportunity. They should have shown TIM triumphant, as he confirmed that Control was possible all along. Not as an Indoctrinated degenerate of a man, but as the one who was correct all this time, and it was Shepard who was misguided in his stubborness.
I mean, it was Cerberus who actually conducted some research on the Reapers. How they communicate. How their Indoctrination works and how to mimic it. How they create Husks and other monstrosities. Their research was what Alliance and other militaries should have started doing immediately after Sovereign was defeated.
Illusive Man's Indoctrination feels shoehorned in the final dialogue, just to make the player feel good about themselves.
That would be a good final twist/explanation. With Illusive Man, not Star Child.