Define "rougher terrain".
Crappy/rough roads? Dirt & gravel?
According to the Trek website 700c x 25 is standard on the Pilot 2.1. I'm guessing you could squeeze in a 27 or 28 tire if need be, but check with your dealer.
As for a more robust wheel, perhaps a the basic Mavic Open Pro rim built up 32 spokes, 3-cross on another pair of Ultegra hubs?