Minutemen + Institute is the most rational choice. Reforming the Institute may be purely headcanon thanks to gameplay restrictions, but it's hard to imagine those nerds being stronger-willed than their new Director, who was specifically put in charge to be a leader, not a scientist.

The Brotherhood is arguably the most fun, I guess it's up to you whether you think they'll be good for the Commonwealth or not, or if their mission is more important. I did the Railroad ending recently and it left a sour taste in my mouth, all they do is set up checkpoints to keep funneling (soon to be extinct, thanks to them) synths to places they're not wanted. No reason at all to side with those clowns.