Sparky, I have to say that I've done a ton of reading regarding the Pilot. It's hands down the best 3 row SUV out there. It's AWD system bests the Highlander, is more efficient, weighs less and lots roomier. I was in a Highlander yesterday and I left completely cramped. The Pilot, not so much, if felt like a 3/4 Honda Odyssey. I can provide links to back up what I typed.
If I had the money, I would plop down $45K for a Pilot Touring Elite. Now.
As far as Honda reliability, well, I'm biased. I have a DD (07 Civic sedan) with 215,000 on the clock and runs like new.
I want to LOVE the highlander, It's a solid SUV, but my preferences would be a Pilot.
EDIT: I did hear of transmission issues AND the V6 burning oil, but it is to my understanding they solved the oil issue with this (latest) generation. As far as the transmission, I've heard sporadically that some are being replaced prematurely. It is NOT a wide spread problem. The rest of the vehicle is bulletproof. Who cares, I would be an extended warranty with that puppy. I sincerely doubt the Pilot will give you problems. Like I said, If I had the smoke, I'd get one right now. (I even have a color picked out, LOL)