obviously with the exceptions of ed-e and rex. I would argue that all companions are "good guys". I miss clover, jericho, and even the nuetrality of charon, the mister gutsy, and butch. There really aren't any new companions that work with the leigon stories.
Because the game hates evil people. I mean, if you kill ghouls and fiends, you gain good karma! Wtf! Evil kill good = evil, good kill evil = good, good kill good = evil, evil kill evil = evil. It doesn't matter if you're evil or not, they'll still attack you. So Obsidian eff'd up hard at that point. It's really hard to maintain a neutral or evil karmic balance, which svcks.