I was just wondering which ones I should stay away from. I'm assuming that, for example, choosing to be a Raider makes practically everyone hostile to you, correct? Any others that make game-breaking changes such as that?

I think, at least for the Slaver one, you can optionally go "hardcoe" and that will be the case; everyone will be hostile and the game will essentially be unbeatable. But it's optional. You get the option when you lay down at cot after finalizing your character.

I usually play a doctor, the boost to medicine and knowing where Rivet City is off the bat is great.

Talon Company may be another to possibly avoid, unless you don't mind removing yourself from the faction now and then.
Rivet City is hostile to Talon Mercs. But I think it's the only settlement that is. I usually play as one of them and when I need to go to RC for the main quest, or for my mod, I just use the console and remove myself from the faction. Then re-add it later.

Being an outcast makes the Brotherhood hostile, thus eliminiating the possibility of completing the main quest.

Nah, Outcast is Neutral to the Brotherhood in FWE.

Ahh, all right. I just remember how noobs whined day after day in the original AS-R Nexus page about this, even though the fact had been mentioned in mod description.

Yes, changing the faction settings B/W outcast + BoS was a change we implemented to let the outcast do the main quest line.

That said, even with the Talon or Raider factions on "hardcoe" (there enemies are yours) it is still possible to do the main quest . . . but it really isn't very easy You have to know the right shortcuts to take in the quest line to avoid certain settlements.