Minutemen - I hate Preston Garvey for wasting my time. That's it.
BoS - I'm tempted to go along with them as I've already helped get most of the stuff for LP and that was my most memorable moment in FO3. They are absolute genocidal, xenophobic douches, though. Danse is the only one that hasn't irritated the pants off of me. Nick V is my best buddy so don't like the idea of him potentially being scrapped.
Railroad - They're like the Fallout version of the LibDems - a bit too idealistic and wishy-washy. Seems like the best choice but they aren't exacly out there defending ordinary citizens from ferals and hostile supermutants like the BoS.
Institute - the first thing I did when I got in there was shoot father in the face with my shotgun. Then I had a think about it and reloaded an earlier save to pursue the quest line. Just got to the point where he's on the roof and I just killed him again. I'm wondering to carry on or reload the save just before again. IMO the place needs to be nuked.