First scenes on the tribunal will be used as a way to get players up to speed with the facts and choices made in previous games. Shepard will be judged and at the same time we will (re)view his/her choices and get to see the reactions of the crowd. There's potential for humour and drama, and we will obviously be given choices on how to respond to grave accusations (with sarcasm? with wit?etc).
Cerberus being an enemy, one wonders why that will be the case. Surely the reapers should focus even the Illusive Man's attention. So the best conclusion I can arrive is that the illusive man doesn't see the "solution" to the reaper's problem the same way that we will be inclined to. What crossed my mind had a sense of balance, but it still doesn't fit a hundred percent.
The idea was simple, that if you give out the collector's base to IM, he will have little to be offended at you, but he may well be driven towards a path of becoming just like a reaper. Keep in mind that IM wants the best course for "humanity", and we should not forget harbinger's rant "we are your salvation through destruction". Both reapers and IM seem somewhat obsessed over the future of mankind. Alternatively, we could have IM being brainwashed by the reapers. I don't like this alternative because IM isn't that careless. The only possible explanation would be desperation.
If however you pick the paragon choice of nuking the collector's base, you really piss him off. At this point, whatever the plans that Cerberus has to get more reaper technology, IM will want to keep shepard out of the way.
The likely scenario here may well be that Cerberus and Shepard aren't really "enemies" to the core, but rather very "aggressive" competitors. They are competing for the same tools to get against the reapers. One could see a game dynamic in here. In choosing a certain mission over another, you are effectively picking a certain "technology" or "something else" to fight against the reapers, while giving IM the chance to get other things. In this race, your choices will have big consequences in the "end battle", who gets the upper hand (if at all) between you and IM over the reapers.
We can think of this like a mini second world war, where both america and russia were not only fighting to win the war, but also to define the post war.
Lastly, perhaps the paragon ending won't be to kill the reapers at all, but to convince them that what they are doing is a huge mistake. Idk, written well it could work.