I fully agree, I think it fits wonderfully in a pavilion about the land. It isn't focusing on avation, that's simply the form of travel. Using your example, should Living with the Land have been in a pavilion about boats, since it is a boat ride? No. Would Soarin have fit as an addition to the World of Motion pavilion, since you fly in a hang glider, a form of motion? No. What really matters is the focus of the ride, not the form of travel.
Besides for how it fits, I think that if it were it's own pavilion, it would've been set up like Mission Space. More of a ride than a full pavilion. I also think that, because the pavilion would've been a bit behind the others (right?) it may have suffered the same problem that Wonders of Life had, lower attendance.
I like the decision they made.
As for your opinion on what changes the queue should get, I wholeheartedly disagree. I think queues are very important. Especially these days, you spend more time on them than you do on the ride. Also, boring queues typically lead people to play with their phones rather than enjoy their trip and socialize with others. That's bad. And no, social media does not count as socializing with others.
I like airports. If they want to theme that way, that's fine by me. But then actually make it look like an airport. Maybe that's what they're doing. But right now, the airport theme is simply an excuse.