I had a laggy mouse for pretty much everything, but I'm using a mediocre 3 year old laptop that has no graphics card (just an accelerator) and 2gb memory and 1.5ghz dual core processor. So, I just assumed it was my computer.
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). I like the base layout as well, the new facilities are good, I REALLY like the idea of having different sized hangars, that adds some more strategy to the base layout design.
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.
The interception I think could be done better. I didn't realize my first craft had been shot down because I wasn't looking at the time, I think it'd be nice to be able to observe the battle a bit better (similar to how X-Com does it, but you could do better, that was my least favorite thing of X-Com). I'd like to see more interaction in the intercept mode.
The battlescape I didn't do much, but I would prefer bringing them out of the ship myself. The battlescape was slow for me, because of my computer, but I played a little bit. 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.
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).