I've been playing the game for I'd guess a total of over forty eight hours now, probably more, and I really like what I'm seeing, so I thought I'd pop in and give my two cents:
My first, and most important (IMO) suggestion is that we should be able to tell the Firebird where to land. Perhaps the soldier equipment code that tell you whether something will fit in a slot or not could be adapted? I personally favor blitzkrieg tactics, going in fast and heavy, so having to slowly move my guys around the map is the most tedious part of the game for me.
This would seem like a game breaker, but really it adds to the realism and it goes into my second point:
Aliens seem to spawn in certain predetermined locations, near their UFO mostly. Having them stand around in the open is a bit weird from a realism point of view and it also makes the game an endless repetition of 'flank and storm the UFO'. Perhaps In the future a randomizer can set different places (such as a house or piece of cover) as their 'central base', that way one has to clean out the houses one at a time. Mind you, for terror missions, it makes sense to find one or two left behind to guard the UFO, but not in crass mission.
Soldiers can't hit anything without lasers. I think everyone else has brought this point up, so that'll all I'll say on the matter. But it really detracts from the weapons I can use, lack of variety and all that.
Aliens won't attack my SAM sites/Radar Towers. I suppose it could be due to the fact that I sent them running with their tails between their legs when they went afer my base, but somehow I doubt it.
And finally, I just wanted to point out that a few details are off in the UFOpedia texts, seeing as their the easiest things to change and realism is second only to game mechanics, I'll probably write up some edits for your consideration a bit later.