To the second point on refuelling: it did seem a little silly that you could fight half a wave but would have to nip home before going back to finish them off. It wasn't exciting and it broke immersion somewhat. I remember needing to take trips back for something as little as a tiny handful of autocannon rounds. Obviously there needs to be some challenge in the air war to make it a game but I'd say that if you're only managing a half dozen craft, the challenge shouldn't be logistics: the refuelling/rearming wait time isn't an interesting aspect of play.
As for your point on lore related research: in another thread on weapons, Chris stated something to the effect that the player shouldn't be facing a decision between researching lasers or filling their xenopedia with lore about the invaders. On a second play through, you wouldn't feel as compelled to study the lore, so you'd get all the combat tech first (in a recent play of XCOM, I did just this and played most of the game with top tier weapons - it became a drag). I guess the issue here is that the single research tree is the helm for too much development. It is the only way to get at the story line, progress through stages of the game and upgrade your gear. These are qualitatively different so probably shouldn't fall under the same umbrella. Xcom Apocalypse had two research divisions, so you could be studying the alien life cycle whilst also designing a new fleet of interceptors. One side of research would seem more important than the other for a while but their significance would alternate as the game progressed.