I like merit points / alternate advancement as it were in EverQuest, but in the post-WoW era, there's going to be a "best" and "correct" way to spend your points, so it's just going to kill customization anyway. "Oh, you specced for increased Contagion duration? That's a DPS loss over improved Fester, you gimp."

I'd really only support this if your merit point allocations were invisible to others.