In my mind (haha) if Shepard picks the red path, he gains control of himself or whatever and goes finish the job in the Citadel, we just aren't shown that. For all we know that dream sequence might have only taken a fraction of a second in the real world.

Well hell, even with the blue or green paths, there would still be something that happens about which we really have NFI.

From previous Mass Effect books, via Mass Effect Wiki; The Illusive Man originally had run ins with Saren back in the day, concerning a machine/device that had been found in the ground. Turians and humans were altered by the device, turning into "priests" of some sort that did nothing but protect the device. When the Illusive Man came in contact with the device, the only thing that seemed to change were his eyes, and a seemingly greater understanding of subtle universal things he did not see before

Imo that device was the beginning of Reaper indoctrination for the Illusive Man

But I'm not sure how it could have gone much differently than that, even if the story was a little different. They had to come up with a reason for the reapers virtually wiping out life in the galaxy every 50,000. Protecting the life forms from becoming extinct is as good as any other reason, right? And it actually does make some sense - though of course we could argue that they could have gone about it differently, but these guys don't have to think completely logically do they? Maybe they just picked an unwise method, but it still makes some sense.

How did you expect the final battle to go. We were assembling a super weapon. At one point it was going to be pressing a button and having it do its thing. Unless you thought somehow Sheppard was going to man the crucible and start zapping reapers out of the sky?

Sure they could have gone a few different ways, but I don't think there was anything wrong with the way they did it.

In fact, after watching the indoctrination video I like it even more. But I'm still not sold on the finally. I chose synthesis - the video seemed to opine that it was just a hallucination the happily ever after part- but I'm not sure why, given that sheppard killed herself - which was also a fitting end for her, imo.