Ive heard a whole bunch of different ideas on this subject, A couple i have really liked and then a couple I have really hated.
One that I really like is that we choose who we get to recruit, Provided they are still alive.
Keep the following on the Normandy SR2 at the start :Legion, Tali, Garrus Miranda and Jacob. Mordin and Thane are too ready to die (Do you get what I mean? Mordin is 10 years older than the average Salarian, and Thane had 6 months to live. I think Mass Effect 3 takes place 2 years after the destruction OR salvaging of the Collector base.) I dont want Bioware to ruin my emotional investment in him by keeping him alive (Thane....not Mordin lol.).
Keep them on the ship at the start. I dont see where Garrus or Tali would go (Or WHY they would go. Garrus and MShep are best friends, and Garrus and FemShep can be lovers.) Same with Tali.
Legion looks up to you as a Hero or something, and he is going to be key to rallying the indoctrinated Geth to our side.
Miranda and Jacob both have a ton of info about Cerberus (Assuming you destroyed the base) and in addition to EDI, Would help you find out where TIM is.
Grunt will go back to Tuchanka. I dont see him staying around. I might need him, But he will also play a huge role (With Wrex) in convincing the Krogan, Free of the Genophage to fight against the Reapers. Let us recruit Liara, Ash/Kaidan, and anyone else we want to from the previous 2 games.
Make Kal Reegar recruitable. His role in ME2 makes me think that they will do just that.
But dont FORCE us to recruit anyone. This team went through hell and back, They can do it again.
I do want to recruit Ash, Liara and Kal Reegar. But past that, I trust Garrus with my life, Im starting to trust Miranda, Kal Reegar would be a great addition to my Soldier ensemble.