I think a few weapons are unbalanced. Take knife.
Its very difficult to sneak up on aliens.
Flame thrower:
its big fun (though I would love to break wooden walls with it) but the problem is you really need to kinda move right up to the enemy... Maybe the range should be extended, or more target squares should be combatted with it. Also i think inferno sweep and inferno is too similar
Grenade launcher:
I think this is a very good weapon actually, you can kill groups of aliens rather nicely with it but the range part is REALLY killing the weapon. Later in the game, the long rifles just pick my guys apart. It makes no sense to run around with a weapon that has such a low range. Sure, you may use it when the map has many buildings etc.. but there are simply better overall weapons imho
Pistol:
I am fine with it, but maybe single shots could be made cheaper?
Bolt Rifle:
Cannonade is very cool, no complaint. The snapshot and precision shot however is kinda annoying... I think it could need a slight boost. But I am ok with it as it is.
Sniper Rifle:
Sorry, it sucks. Headshot takes up 24 points? And normal movement is 31, so what am I supposed to do, take a position somewhere on the map.. and wait. But the aliens will shoot at me too and hit me much easier with their long range weapons... and if i actually move, i can do only one shot, which normally miss. Compare this to a weapon that can fire multiple times.
Grenades:
Not sure... they kinda roll around and miss too often, and they block a hand, thus preventing the use of a normal weapon kinda...
Submachine gun:
This is kinda the best weapon, even though its only secondary.
I can fire SO MANY SHOTS with it, i can happily use reaction fire... yes, it doesnt do a lot of damage, but i think firing SO MUCH is simply better. sooner or later the alien just is dead.
Missile thrower:
I think its underpowered. The exploding missile hardly kills an alien on first shot for me. And reloading takes a lot of points... and we cant destroy buildings with it... and there are no waypoints... and, well actually, the other weapons are just better!
Not sure about the other weapons... I am not yet an expert but i think the machine gun is useless, especially compared to assault rifle (which is much better) and the submachine gun is a lot better than the machine gun too.
I think these issues should be considered. It would be cool if weapons that are too similar could be modified a bit to reflect different needs. I would also like to see a somewhat heavier pistol-type weapon. Something like a huge desert eagle or magnum or something, maybe with a bit longer range and power but heavier handling cost.
Also what could be fun, a kinda whip that has a limited range (but higher than knife). Something like an ultra-thin whip but supersharp... guess you know what i mean
Anyway, in general I am ok with the weapons because I get to choose - and not elect those weapons that I feel are less useful