Another point: make the factions make sense in the context of the universe.
Quite frankly, one of my greatest sources of annoy and amuse is the Lyons / Outcast debacle. It seems to me as if Bethesda tailored Lyons' Brotherhood to be that likeable faction, one every good gamer wants to be a part of, with knightly armours, guns, a giant robot, a citadel! But to me, it end ups trying too hard to be likeable, with medieval overtones, middle ages speech and that gung-ho attitude so cliche nowadays.
Outcasts on the contrary, seem to have been made with evil in mind - gruff attitude, black/red power armours... but in the end, they come off as most professional and most useful, since it's them, not Lyons, who patrol the wastelands and nuke creatures that might hurt you or others.