I could be wrong. (I was wrong once; it was an interesting experience. That is, I thought I made a mistake once, but I was wrong.) 🙂
I completely agree that any good game should be as flexible as possible, but... within its scope? Trying to make every game for every stripe of player just dilutes them into mush only distinguishable by the title screen. And to me, PvE and PvP are a huge, fundamental fork between game types.
Maybe CoX2 should be fundamentally PvP, hero vs. villain, with well-designed mobs to fill out the experience. But that would be a very different game from one resolutely designed as PvE, with an added player "enemy" option that is anything but, and then completely vanilla arena PvP shoehorned in. There would have to be draw to have alts on both sides for that to work, though.