So, what's the deal with green reapers? They keep running around doing absolutely nothing. I have seen them stun civilians couple times, but they don't touch the actual soldiers at all. They can be surrounded and shot at point blank range without much risk... which I suppose is a good thing, because damn, they take a lot of effort to kill. Nearly anything early-mid game seems to be resisted and once you actually start to punch through that armor, they regenerate. It's easier to melee them with stun batons than trying to shoot them.
Still, if they actually attacked and were a real threat, they'd be nearly impossible to take down without major casualties. Would need some defensive nerfs, as "normal" reapers go down easily, but these bastards are a nuisance.
Also, is it just me or is there never enough Alenium for... well, anything? Building weapons for even a single base worth of aircraft takes dozens of ground missions (and that's not counting what you spend on building the airacrafts themselves). It does seem to get a bit better with bigger ufo's, but still, fighting medium/early heavies with basic weapons is just weird.
In contrast, money is trivial. Dissasembling UFOs gives huge amounts of cash, in addition to normal monthly income. It feels like I'm too rich - and that's with airstriking quite a few missions. I could easily cover the entire world with radars and still have tons of spare cash. Unless late game items get much more expensive... but then again, bigger ufo parts sell for more, so there's no difference.
Weapon balance was already mentioned. It really does feel like half the weapons are useless. Harridans can snipe you from the other side of the map, whereas your snipers are pretty much a joke. Machines guns do almost no damage while costing majority of TUs to fire. Shotguns... nah, just stick to rifles, longer range, similar damage, won't get you killed by return fire. Pistols are meh, but worth it for shields.
Props for making vehicles useful, though. Really helps to have a tank as Harridan bait, being able to take all those nasty shots and fire back doing major damage. Still - is Saviour tank supposed to take more transport space than earlier vehicles? Had to bench one additional soldier to fit it in, which makes me doubt if it's worth it.