Remove fat cap. Smoke and rub will not penetrate the fat cap even if it is scored. Butts have enough internal fat and connective tissue to baste from inside. By removing it, you get more smoke flavor, more bark, and more pink purple smoke ring...makes a much nicer presentation in the tray too.
One of the best reads on preparation of a pork butt is here: http://www.virtualweberbullet.com/porkbuttselect.html
it talks about the fat cap and whether to leave or remove.
Also, I keep the removed fat caps and add them to sausage I make when I need more fat...it doesn't go to waste.
If you really want to find out what works for you, do two this weekend and judge for yourself...one with and one without.