I've been following the last pages with the discussion that Shepard was needed by the Catalyst to make a decision. And while I was initially rejecting this flat out I've come to accept that this very well might be the case after I thought about it like the ending of Terminator 2. Remember that? The battle is won and Sarah and John Conner are alive, the T1000 is ' dead' and their saviour Arnold T800 is still 'alive'. With the mission parameters fulfilled the T800 instructs them to have him lowered into the steel as he can not self terminate.
One could argue that after the crucible managed to dock at the citadel the program of the catalyst got a new set of instructions where it is to give an organic the choice of how to proceed. What bothers me about this is what's been mentioned before that we've got our faces rubbed in the fact, repeatedly so even, that we are beneath them so it's a bit hard to imagine that their core programming allows for an organic to decide the fate or not just all organics, but also the Reapers themselves.
What also bothers me about this that it makes no sense for TIM to be involved in the citadel. As I see it the Catalyst had instructions that as soon as one organic made it into the citadel then that organic would not be attacked anymore. After all he is there is to meet the catalyst and make a choice. Otherwise the Catalyst could have the entrance of the citadel packed with husks, banshees and what more.
This begs the question what TIM is doing on the citadel? To be honest his entire role here is a bit weird. First of all an entire army of the alliance stormed that beam to get to the citadel, but only 2 men, both wounded, make it. And then there is TIM without a scratch on him. While this is possible as he is indoctrinated and would not be attacked by reaper forces, the catalyst basically must have TIM instructed to come to the citadel. But why? TIM serves no purpose. He is indoctrinated and as such can't actually make a decision from his free will so as far as the catalyst and the choice is concerned he has no business on the citadel.
And while you could argue that TIM basically had it right, depending on your preferred ending of course, there was still no point for him to be there. Everything the catalyst would have wanted to know from TIM he could, and basically already had, lifted straight from TIMs brain.
And if an organic is supposed to meet with the catalyst why does TIM try to kill Anderson and Shepard, or rather is allowed to try and kill them as he should be indoctrinated. Still from the talk between Shepard and TIM it's clear that TIM is not fully indoctrinated, but if he is not fully indoctrinated how the hell did he make it to the citadel? For sake of the story I can fore go some discrepancies, but this is a tad much.
Oh, I rewatched a bit of the ending and for the people in favor of a control ending (although the post by Isac23 one page back is an awesome argument against that in itself) and this is what Shepard himself says "You're playing with things you don't understand. With power you shouldn't be able to use.". And while I myself said that the Catalyst doesn't have a reason to lie to Shepard when he presents the choices it seems a bit odd that Shepard would go for an option he was so against when TIM wanted to go for it. I suppose you can argue that Sheplyst would be able to understand things, the thing is that the human Shepard wouldn't want to able to use that kind of power.