I agree that the third row seating is not a great idea in the Pilot, and is only there as a way for the Pilot to inch it's foot in the door in the full size segment, where is won't otherwise hang anyway, and it is not really very well executed in the Pilot, being more of a hindrance than a help to most folks who choose to own Pilots. If you really want third row seating, the Odyssey is a way better option all around. I think Honda is realizing this, and the Passport re-intro is a precursor to dropping the Pilot. This would tighten up Honda's fleet overall in the mileage department, just a smidge.
One thing I have not seen discussed here much is something I think makes the real difference between choosers of the CR-V and of the Pilot. That's the fact that many CR-V owners picked them because they were looking for the best possible vehicle for sitting in rush hour traffic. Commuters want relative comfort, good safety, entertainment, and excellent mileage. For those of us that are city dwellers, this is a huge consideration. The Pilot's mass has pros and cons in this hunt, but it loses points for mileage and for being unnecessarily large. If you are a daily grind participant in this race you know 99% of the cars in traffic are carrying one person. Most of the rest have just two. It's why HOV lanes are such a lose-lose waste of space in the race to and from work. No matter what incentives the government's pencil pushers can ever offer, this will never work, because people have certain preferences and requirements and are not willing to adapt.
I think the Passport makes sense as a choice for those commuters who want the larger mass at any cost or mileage, but I don't see it cutting into the CR-V segment at all. But I also don't see both the Pilot and Passport staying in the lineup, they are just too similar. So I think the Passport, which removes some of that mass that the third row seating requires and points those folks who want it towards the Odyssey, and takes away the pressure for Honda to keep the Pilot by still offering all the other benefits at a slightly lower price and size. Meanwhile, the CR-V can retain its position at the top of the heap in it's segment, which is as the perfect commuter/rush hour car. I suppose Honda could conceivably move forward on a full size entry, a truck and an SUV, maybe even with a V8, but I am kind of skeptical of that. I think the Pilot will go away once the Passport takes hold.