When shopping for our Pilot, we looked long and hard at the 4Runner as we both always wanted one.
Here's why we went with the Pilot:
1. Cargo space. For our needs, we would always have had to lower the rear seats on the Toyota. Not so with the Pilot. It's amazing what a few extra inches can do. (easy everyone)
Cargo room is very, very close between the two. Of course, your situation may be unique.
2. Standard equipment. To get side and curtain airbags in the 4runner you had to go to the limited level. That was a HUGE price jump! All levels of the Pilot had this as standard.
You had a point up until last year. Side Impact Airbags are now standard on the 4Runner, all trims.
3. Dealing: Toyota wouldn't, Honda would.
Can't really argue with that, you'd be lucky to get $1K off MSRP on a 4Runner. However, the 4Runner has, out of all SUVs pretty much highest possible reliability rating you can find. Actually, it might be the most reliable SUV out there. It is almost rare to find any with an issue and the resale is incredible. The fit and finish is amazing too. They're actually built at the Lexus plant in Tahara, Japan.
One thing the Pilot did seem to have a slight edge on the 4Runner though was the front seats "seemed" a bit wider than the Toyota.
he Pilot has been out since...2003? Pretty dated.
Same with the 4Runner.
So CX-9 it is.
Why mess with a good thing?
You've got a point though, but comparing a CX9 to a 4Runner is not fair. One is a car with an AWD system for the odd bit of inclimate weather. The 4Runner is a truck based SUV. The V6 also gets surprisingly good fuel economy for what it is - pushing 19MPG in town and low 20s on the highway.