-Better interior. I agree Mazda interior is nicer
-Better/more usable third row. i don't think either are that usable - both can be used with kids for short trips, that's about it.
-Driving like a car vs driving like an SUV (for the Highlander). This is where Mazda shines for sure.
-Seem less room (narrower) in the first row. i think you're right so you have to see if you want that narrow "cockpit" feel or the "roomy" feel. this is personal preference.
-Less comfortable drivers seat. i think if you want cushy/smushy, Highlander is better. if you want a more supported feel, Mazda may be better. but the Mazda has only 6-way directional adjustment plus lumbar support adjustment. people have complained about this. go sit in a CX-9 and adjust it to your liking. if you can't find a comfortable position, CX-9 is probably not for you.
-Less expensive.
-Better gas mileage. Real-world reports have been lower than EPA numbers on CX-9 so this should not be the deciding factor for you in the end. please note that 2017 Highlander coming out has a new engine (same as in Lexus RX) so you may want to wait for that one.