The trial idea for Shepard is non-sensical, at least as a starting point for ME3. If the Council didn't arrest Shepard for simply being with Cerberus when they first met, I don't see why they'd arrest him later, when he hasn't done anything significantly criminal since then. More over, I'm not sure they could avoid trying him publicly, and Shepard getting publicity means the Reapers getting publicity. The Council wants the galaxy complacent, and giving Shepard a microphone is a bad way to do that. A trial midway through ME3 might make sense, but not in the beginning.
As best we can assume, ME3 will involve open war against the Reapers, and will therefore involve mobilizing the galaxy against them. Here's my take on the likely shape of ME3:
Mobilizing the galaxy against the Reapers will require Shepard's credibility not being undermined by his Cerberus affiliation. It will also require him/her presenting undeniable proof that the Reapers exist and are a mortal threat to all life (before they actually start attacking en masse, since that'd likely be too late to fight back). And, from a game development standpoint, it will require converging the trajectories of various decisions made in ME1 and 2.
Therefore, I think the beginning of the game will involve searching a long lost planet or facility for Reaper evidence, and in the aftermath of that mission, TIM and Shepard agree that Shepard must part ways with Cerberus. Despite what some people say, I don't think TIM will betray or undermine Shepard, because so far he/she's the only one able to fight the Reapers. TIM is too calculating to simply activate a secret kill-switch on the galaxy's potential savior. Instead, I think TIM asks Shepard to act as a Cerberus double-agent, feeding him intelligence and undermining alien races so humanity (and Cerberus) have more control over the alliance Shepard forms.
Either way, I think Shepard goes back to the Alliance (at least officially), and the story missions in ME3 become two-sided: the paragon route of trusting and strengthening other races as you recruit them, or the renegade route of helping Cerberus undermine and manipulate other races into basically fodder for the Reapers. I think it could be cool if TIM eventually turns on you, but I think you should have to deny him repeatedly before that occurs. He doesn't really care if you disagree with him; he does care if he thinks you're building a weak alliance.
As far as squad members, I think the minimum for canon should assume that Miranda, Jacob, Garrus and Tali survived, as did the Normandy crew. Those four, plus the crew, give solid footing for whatever story BW comes up, and lots of options if tension develops between Shepard and Cerberus. It would make sense if Thane, Mordin, Legion, Samara/Morinth and Zaeed left the ship, if they survived. It would make less sense for Grunt and Jack to leave, since they seem to have nowhere else to go. I'm not dissing characters (I would love to keep a lot of them), I'm just saying some people are going to have to get axed one way or another.
The beginning of the game is really as far as I'd care to speculate at this point. Regardless of which characters you think should stay in ME3, I hope Bioware doesn't introduce a lot of new characters just for the sake of new characters. People enjoy having a history with characters, and Shepard did recruit some of the best in ME2.
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