Does ToR have separate PvE and PvP skill trees? Or does this nerf affect both PvE and PvP? Could get messy.
Nope. You basically have your set skill tree and what's optimal for PvE and PvP aren't necessarily the same thing. So you end up having to respec to do one or the other. That being said, you can probably make due in PvE with whatever you choose for PvE as you can always out level most things in the game aside from the end game bosses. But since you can bring a friend to any mission, you can still get through anything you might need to one way or another.