The best thing to do would be to look at the squadmate condition as a 'what would they be doing' kinda thing. So, the confirmed ones dont need to be accounted for, Garrus, Tali, Ash/Kaiden, Liara. That leaves us with:
Wrex - We know he will probably be leading the Krogan Army, Urdnot being the strongest clan
Grunt - I see no reason why Grunt can't be with us, the only thing stopping him is if he agrees to be 'cloned' to create an army of perfect krogan
Jack - I don't care if Jack is back or not, but, in all honesty, she has no where else to go, no home or anything like that.
Jacob - I think he might stick with Shep, but then again, he might A) go back to the Alliance and you meet him and his squad, or

Stick with Cerberus and you meet him and his squad
Kasumi - I dont think she'll be a squad member, can't imagine her doing anything else, but she's DLC
Legion - We've seen him driving a Geth Car thing, but that doesn't confirm wether he is temp or not. My guess is he would become the leader of the Geth, rallying them. Of course, he is the only mobile platform, so he would have to re-link back with them somehow
Miranda - I really want Miri back, but I think Cerberus might have her somewhere. She eiher left, and knowing how much she does about Cerberus means she would be a high priority 'kill' target, or she stayed with them and became indctrinated
Mordin - I have no idea about Mordin
Samara/Morinth - They'd probably be doing their own thing on Thessia, maybe temp squaddie
Thane - Thane is dying, so I think he will be in no condition to fight
Zaeed - I think Zaeed will be fighting, but not with Shep, as he is DLC
That's my thoughts on it