Only difference is a Honda Pilot will cost considerably more money up front than an Explorer. To the tune of over $5000 more on average than a similarly equipped Explorer of like year and miles.
I never liked anything Honda made (with the exception of some of their motorcycles). There's really no innovation in their cars and SUVs...Most everything is a copy of something that another company already had in the market. They just take someone else's design and perfect it, or so it seems.
If you like the Explorer's looks, ride, handling, etc. you'll still have a good chunk of change leftover to put aside for any possible (and I emphasize possible) mechanical problems that may occur. Or, just get a real good extended warranty such as a Wynn's Extended Care that'll cover you to 100,000 miles nearly bumper-to-bumper.
For me, I do nearly all my own mechanical work, so I just look for the best deal, regardless of whether it needs some things fixed. So far, nothing has really failed on mine, and I drive the wheels off it! I've got over 80,000 on my '04 already, and it's been great. Only thing that broke (and still hasn't gotten fixed) has been the lumbar adjuster on the driver's seat. I may even send that out to get done...I hate tearing seats apart. How sad is that...I'll have no problems putting new timing chains or a transmission in one of these, but a little cable inside the seat is too challenging that I feel I might lose my patience with it?