Welcome to the forums!
I really like the idea of having pilots for each craft, I'm hoping that they will eventually have stats that affect their piloting so you can pick up different pilots for different crafts (like some are better at combat, and others are good at landing in advantageous spots for battle).
Something like this. I believe I read something about a combat skill and a hidden survival skill and something else, but stats for pilots is planned (I think so, anyway)
One thing I always wished you could do in X-Com was set up your initial base layout, since that is something you could conceivably do if you're there starting up the group, I realize that's not really the case in UFO:AI though. Still, I think it would be nice.
You're not the first person to come up with this complaint, you probably won't be the last.
The battlescape... Orientation was a bit weird, it was difficult to exactly move and things, but I think that might have been due to my computer's slowness.
I agree. Is there a "result to default view" button, or plans to put one in?
The only other problem I had was with the layout of the geoscape, it's not laid out to be incredibly user friendly, I had to go searching for a lot of things that would have been nice to have them be very obvious, I do like the timing and zoom controls though. I wouldn't mind seeing the stopping of time going away though (just my X-Com purist showing).
I think pause was added just recently (the last version I played was 2.2.1 though, so yeah). 5 seconds is still so slow as to be the same though, really. 12 seconds to a minute, 12 minutes to an hour. It can take a dropship more than 20 hours to reach your destination, do the math. Might as well keep pause anyway though, no reason removing something that doesn't detract.
Personally the Geoscape has really improved - I really like the new swivel to events tab thing (although loading a game while I was swivelling or loading a game being swivelled caused the camera to lose it, or maybe I was dragging the mouse). Would it be possible to have the same for bases (IE a menu showing all bases, but the menu can be closed, same with dropships. Also maybe like the statistics a "global production" setup as well as an automatic-transfer-equipment-to-base-setup (Say, you have a manufacturing facility pumping out ammunition or something and getting it auto sent to the base with your dropship teams, or whatever).)
The highlight nation borders setting was a bit too bright for me - would it be possible to get a brightness setting? (Then again I'm probably the only guy who thinks this, being blinded by the Skype's colours)
/rant
Anyway, tldr: Welcome new guy, agree, agree, whine, whine.