If you want to enjoy driving your vehicle, get the CX-9. If you want to enjoy driving others, get the Highlander.
Even this argument about passenger comfort can go to the CX-9. The CX-9 arguably has more comfortable 2nd row seats, with deeper floor wells, and more supportive seats. With captains chairs, the Highlander has a more open feel though. And if you do use the 3rd row, the CX-9 is actually better, plus more room behind 3rd row.
I have 2 kids, 5 & 3. Will rarely use the 3rd row anyway. Cargo space behind 2nd row of CX-9 is plenty for any road trip.
It's other qualities that have me on the fence.
Highlander is better for...
Long term reliability and longevity. Question for me is how long I plan on keeping it. I don't drive that many miles
Resale value
Looks more rugged like an SUV if that's what you want
Certain available features, separate opening hatch window, etc.
More HP for high speed passing power, towing capacity
Interior storage
Better AC?
CX-9 better for...
Driving dynamics
Interior style, and material quality
Exterior style (subjective)
Low end torque and responsiveness
Total leg room across 3 rows
Fun image, less mommy mobile, less minivan substitute.