While it is true that WoW's PvP system is more or less "bolted on" Blizzard wouldn't have done it if they didn't believe that was what their players wanted. Nearly every PvP addition to the game has been wildly popular so why wouldn't they continue bolting more on.

Your point about the separation of PvE and PvP is perfectly valid. I myself used to be in a high end raiding guild pre-TBC that also PvP'd together with great success. When cross faction battlegrounds were released our guild became a point of pride for our server.

I miss that but I understand why it had to go - the people in our guild that valued PvP the most were absolute addicts. They would raid for 30+ hours a week and then PvP on top of it. It's not healthy. But if you wanted to be good at PvP you needed the gear. People who couldn't keep up were left in the dust. And I mean in the dust. As a Mage I would stack nothing but +dmg and crit gear and two shot everyone. Survivability was hardly a concern because people would die too quickly.

Nowadays it's all changed if you want to just PvP and nothing else you have that option. I would have quit long ago if it weren't for that fact and so too I believe would many others.

The only hope for integrating PvE and PvP more closely now is with world PvP - and if you've been keeping up with WotLK news you know that Blizzard has something up it's sleeve.