I have 2010 Honda Pilot. I have tried the roof rack and the hitch rack option. I would say that the hitch rack is the way to go. The Pilot is really tall to get a bike up there, you would need to bring a small step stool. I have the running boards too and they didn't cut it. I'm about 6' tall.
Now having said that...I now own a T2 rack which has been nothing but awesome. You can get a swag or sport rack, but make sure you get a rack that is 2 inch. I don't suggest getting a rack that has a 2 inch adaptor. The way the Pilot hitch is designed, it doesn't play well with the adaptors. I had a sportrack with the adaptor and after a month, the adaptor was falling apart. The hitch of the Pilot would cut into it.
The T2 is more expensive, but I think for the money it is worth it. You are going to going to put a 3 grand bike on it and be traveling on the freeway. I want to make sure my bike to be safe and secure. My buddy has a sportrack and the other day on the freeway, when I was following him, the outside bike clamp came loose and the bike was dangling off the rack. If it wasn't for the straps that tie down the tire, the bike would have ended up on the freeway under my car.
As far as security...the T2 comes with the Hitch lock and locks for the carriers. Other carriers might not come with that...so figure in another 50 dollars or so onto the price. I also went down to the hardware store and made a cable with loops at the both ends as an extra precaution. I just weave it through the bikes and then use the hitch lock to lock it up.
If you look around you can get the T2 for a reasonable price. Use ebay bucks and ebates. I got my T2 rack new for 300 dollars shipped to my door on ebay.
