Railroad hands down. They're a minor faction on the level of the Great Khans but considered the fourth major faction in the exact same manner as all the other factions with no care for them being a resistance group and not owning/being a large organized millitary like the other factions. They even have to piggyback off most of the Insitute's quests because couldn't be bothered to give them anything. Thankfully there are at least enough mods that you can actually make them feel like a functioning main faction if you want.

If you ment bad as in evil... I... uh... Its kinda obvious.