Pathfinder Adventure Paths make it worth it. I'm running Kingmaker for the second time. Also, a lot of the Alternate Class Features are really fun to use. There is less emphasis on multiclassing and prestige classes. For the fighter and flying enemies bit, I didn't see it as too much of a limit in normal play.

Either get a potion of fly, or have an alchemist in the group and drink one of their extracts of fly.

That said, the Advanced Player's Guide classes are a lot of fun, Alchemist and Witch especially. The Ultimate Combat and Ultimate Magic classes aren't quite as interesting in my opinion, I'd only get those books for the Alternate Class Features.