As for the indocrination theory, this is an issue I see:
- The whole thing being an illusion would leave the real Illusive Man out of the picture, which would feel very weird since he's a crucial character.
Also, Bioware concept arts for him in ME3 reveal they wanted to make him look like an hulking synthetic monster. Probably used for the final boss battle.
They then scrapped the idea, because they wanted him to remain human. With that, they probably dumped the whole boss battle idea. (source: ME3 artbook).
As for the choices, aka Bioware trademark wheel:
- I get that the Blue choice is for Paragon, which feels good (Reapers are gone) and has heroic sacrifice in it.
- Red choice is for Renegade, since it has guns and a "kick-ass" feeling.
But I still dont get why creating the extra sequence with him alive. It really confuses me as it makes this ending look like the best one, while Renegade choices usually aren't.
- Green choice is the expected - complete the game 100% for extra candy - ending.
But it's very weird. They wanted something like a win-win situation (in fact, problem is kinda "solved") but I feel something got wrong in the writing, and many fans disliked the whole idea, thus depriving this ending of its special qualities.