It all depends on where your priorities lay.
If you do not care about the price difference, you may not care about the other monetary factors but here are the comparison points. To be brutally honest, hybrid SUV's do not do too much in terms of boosting their gas mileage. In terms of the hybrid Highlander, the best comparison to the kind of gas mileage it will get is that of an ordinary Mid size or full size sedan with a normal engine. In return for it's improved mileage, the hybrid SUV's take an enormous hit in HSP/Ton (Horsepower per Ton) and therefore are much slower vehicles.
The Honda Pilot, while not having a hybrid model incorporates some pretty spiffy technology that allows the SUV to run on only 3 or 4 of it's 6 cylinders when it can. While this will not result in the same boost in mileage that the Highlander's hybrid engine does, it does allow you to save gas when you want to without severely and permanently affecting the vehicles power.
Other than that, both vehicles have comparable interiors and exteriors and really comes down to which one you personally find more attractive. Both of these companies have excellent reputations and either choice is a pretty solid one.
If I had to choose, I might buy the new Pilot, but I may be a little bias as I am a proud owner of a 2005 Pilot EX!
!!