The mouse/kb is faster/more efficient than the controller, at least outside of UFOs. The mouse struggles with height differences inside UFOs as you just noted. It's a pretty good tactics game and I like the strategic layer - I hope they make an X-Com EU 2 sequel. I'd give it a 7.5 on consoles and an 8.0 on PC mainly due to control issues.
If you're looking for X-Com clones I know of no less than 5 of them you can check out. You can find the links and some other news
here.
There are a couple major games left in 2012. There's MechWarrior Tactics, Skulls of the Shogun, Ragnarok Tactics, and 2nd Super Robot Wars OG. I'm really looking forward to Skulls of the Shogun and 2nd Super Robot Wars OG. You can check out the tactics game list I've been maintaining
here.