Ok, I'm not saying that IT is my favorite thing of all time or anything, but why is it always an us vs. them thing in every discussion? I'm not saying that's what the OP's doing, but IT always has been a really well thought out theory and just as good as anything else-in many ways it was always far better than anything we got. It just was widely criticized for not having an ending-the game was released without one if IT was true. Well, funny thing here. No matter what the game was released without a real ending and for me, the ending is still non-existent. I may not have ever fully embraced IT, but it has merits-it still has merits.
Does the Leviathan ever say the kid is the catalyst and that he is the "intelligence"? I don't recall him saying that. But, also consider this. Leviathan comes before the ending. I know that IT adherents often have different ideas as to where indoctrination takes place so several things could occur here.
If indoctrination occurred before ME3 (and believe me, it does make some sense), the kid in the vent makes more sense-he really does not make sense now. Shepard in detention and all that crap at the beginning makes more sense, since it really doesn't make sense now. And so on-crucible is a childlike, dream device. Does it make sense right now? Not to me. It's a weapon, no it isn't. Well, by all means let's just make this thing that could annihilate the galaxy since we don't know what it does.
Ok, then Leviathan-main point. If IT-it could all be a ploy to explain away the reapers and since it's main reason for being in the game is to provide reasons as to why the kid/reapers are doing what they are doing, it totally fits with IT. What is indoctrination used for? Well, obviously it's used to get the person to do what the reapers want them to do. How does the appearance of the Leviathan change all that? Many people see it as reinforcing that. Many people see Leviathan as helping make a case for synthesis. Well, what does it seem the kid wants? Synthesis.
So, if the reapers want synthesis and indoctrinated Shepard, what would they work to get Shepard to do?
And why didn't they use TIM? He was there already. Wouldn't it have been really funny if TIM was not indoctrinated at all, but that Shepard was?
I'm going along here with the assertion that the kid wants one of the choices made, first off. Any one of them will work, but they aren't all his "perfect" choice. If synthesis is, then nothing in Leviathan nor the EC smashes the idea of IT. He could have indoctrinated all of them-TIM, Anderson, and Shepard.
Consider this too. TIM cannot control the reapers, because the kid says they control him already. I hate control, but this does imply that indoctrination is being used to keep TIM from controlling the reapers. It's not the preferred choice. Both TIM and Anderson were on the citadel first. Anderson is apparently also under their control perhaps and he wants to destroy them-so, Shepard is forced to shoot him. The only chance they have for synthesis is Shepard.
Again, I don't totally love IT, but it's not garbage at all and nothing in the game post-EC and post-Leviathan smashes the theory at all. In fact, I think it all does the exact opposite. Make a choice and just look at how sweet the slides are-that doesn't seem realistic to me.