Ok everyone stand back, I'm going to attempt the impossible...
I will now try to defend Mac Walters and restore your hopes in the indoctrination theory (it's still speculation though, and quite possible that all this is just an oversight on BioWare's part, and an intentional plot hole that is there simply to make the crappy ending possible at all).
1. Why does TIM DELIBERATELY stand in hepard's line of fire. He can only be shot (assuming you don't talk himself into an hero) BECAUSE he stands right in the path of your bullet.
Was that because the indoctrination theory is right and this was SUPPOSED to happen? What keeps bugging me is the paragon/renegade mixup. Destroying the collectors is seemingly renegade but it was the choice Anderson would have made, and (through EMS) ties to destroying the collector base, which is a paragon choice.
2. What the app said. You know, that silly flow chart with "FIRST MATRIX" written on it, along with "LOTS OF SPECULATION"
Let's assume for a moment, that this is indeed intentional. Everyone's reaction to "first matrix" seems to be "more like the scraps of matrix 2 and 3 cobbled together with duct tape and chewing gum" - and that's because you instinctively think of the ending in which Neo flies away, vs the crappy deus ex machina that we got in matrix 2 and 3.
But what if...
What if Mac was thinking a bit earlier. That scene when Neo takes a full clip of .50 AE to the chest, point blank, and everything seems lost. And then he gets up...
Also - I've been thinking. The ending was edited, and seemingly crucial parts were cut. You know - your squadmates getting obliterated, extended talks etc. Why is that?
The widely accepted belief is that BW lost their marbles for good, and in a last ditch attempt to make a "clever, artsy" ending, opted for "Nietzsche meets Picasso".
The other, that I've been thinking about more and more recently, is that putting more content into the ending, actually works AGAINST the "secret indoctrination plot" by dilluting the ending (so to speak), and if you allay too much of the community's fears, you don't get them talking about the course of action you WANT them to talk about.
Still, this is just speculation, and I have no way of knowing if this is actually relevant, or simply more crappy writing by Walters and Hudson.