There's almost no such thing as too much wheel travel, but if wheel travel supercedes available room in your fenderwells, you'll have create extra clearance, run smaller tires or limit your bump travel.
During a recent desert trip, I found out that my front tires are fully capable of fender well contact, evidenced by the wrinkles in the vertical face of the fenderwells above the wheels. At first, I thought that the frame was flexing enough to tweak the sheet metal, but scrape marks from the tires point to the real culprit.
Sheet metal surgery will be my chosen solution. Long-travel performance in the dirt is something I don't want to compromise by limiting my bump travel, and I don't want to go any smaller than the 33's I'm running right now.
The first photo shows the wrinkled fenderwells, and the pic with the fender removed is for comparison.