Hmm. Noone died for me while still on the ship. Choices for squad leaders are pretty easy to figure out just from character descriptions.
I had Legion go through the vents with no problem, and Jacob as the other squad leader throughout simply because I never use him. (Although, I'm pretty sure either Garrus or Miranda work just as well.) As for escorting the prisoners, anyone who's loyal works. I chose Mordin. Jack can get it done without being loyal, but she sacrifices herself in the process.
As for having someone stay back and defend before the final boss, you don't really have to leave anyone. It seemed like a pointless decision, as whoever you dont take to the last fight with you goes back to defend anyways.
I need to do a second playthrough with my save file from ME1. Never got the save to transfer.
You definately should. The game seemed like it imported a lot more variables than it suggested, and seeing Wrex again is kinda awesome. Also, I wouldn't really want to go into the third game without him having survived.
Unfortunately, I got Legion killed the first time, so that just won't do.
How'd you manage that?