Now this is an interesting topic. Hackett and TIM. A moral conflict in ME3 would be very interesting, though since something like that would be a very large choice, and most likely severely affect everything after it, it would have to be fairly late in the game I think.
I see the whole equal and opposite thing, they're both top figures in the 2 extremes, both command figures, they are both brilliant at their respective commands, they are both incredible at strategizing, and they are both done by extremely good voice actors, and we've had ME1 with the alliance, ME2 with cerberus, so it may be possible that we get some sort of choice in ME3.
As for me, I'd take hackett over TIM any day, though TIM does get a fair few points for being one of the few people in the galaxy who takes the reapers seriously and actually bothers to get off his ass and do something about it. Ok, well actually he mostly sits down and does everything through screens and communication, so bad example, but you get my point. Whether hackett believed shep after the destruction of the normandy SR1 I do not know, this may well have been answered somewhere already, if he did, then there wasn't exactly anything he could do to help shep without losing his command, and having someone who believes him in that position could be very handy. If he didn't believe shep, then although I'd be very annoyed with him, that still wouldn't mean i'd pick TIM over him.
I do wish sometimes the alliance could take a page out of cerberus book on 2 things, and only 2 things. 1) believing in the reapers 2) what was it that jacob said? Ummm, oh yeah: "When colonies go missing, we don't commision a team to write a report to figure out what the hell to do about it. We just go and find out."
Though the IM might have the potential to be a small antagonist in ME3, I seriously doubt he'd be anything more than a small annoyance compared to the reapers, even if he sides with them, which is not completely out of the question

. There could be a possible moment to choose one or the other, after which the one you don't choose becomes your enemy.
By this I mean the sort of thing where you choose one to fight the reapers with, and after the reapers are done and dusted, if you've sided with the alliance, you build a perfect galaxy, if you side with cerberus, TIM takes over the galaxy, with shep in a position of power, something like that. I know it's not very likely, but if this did happen, could be something like that