OK, thanks for the support, guys!
You deserve it man, as I said, you've made something new and awesome and it's the unfortunate side-effect that it makes people care and comment, and it's more natural to say: "fix this" and it's also shorter otherwise "I like this, and that, and this too, oh, and that too! and..." just takes too long. It's odd, but I think as a creator you have to take pride in how much comment you get, regardless of what it is, because with the exception of "This sucks!" which is pretty rare, it all means that somebody cares about what you did.
@Arthanor: Interesting. Just to complete your proposed model, when do we get to buy axes?
When you've completed "Contacts: Hardware store", which is actually called "Improvised Weapons" in game because "Contacts: Hardware store" sounds stupid. That research could give the logistics officer talking about how she had to hire lawyers to make a case to the bureaucracy that using improvised weapons to kill monsters was ok and not animal cruelty, and similarly that axing a terrorist was no worse than shooting them. Now that it's gone through, the quartermaster can go to the hardware store or military surplus and buy axes/hammers/machetes/combat knives/etc. for the agents to bring on missions.
The above, plus interrogation of any Black Lotus cultist (or maybe not the kimono guys but only the ninja looking guys?), enables the "Contacts: Katana Ninjas", actually called "Historic Weapons" to sound more sensible, which unlocks katanas, tonfas, throwing knives, maybe a broadsword for the HEMA enthusiast, etc. This one could be a report from the quartermaster, saying that he had an argument with the logistics officer about how it was no worse to slash a monster with a Katana than axing one with an axe, after an agent questioned his selection of "weapons" and laughed at him for running a hardware store instead of a proper armory. Upon verification, the legal precedent should hold and he can now provide you with proper (old-style) weapons instead of having to use tools.
All these weapons would available from day 1 in the UFOPaedia and can be used when picked up, but require the above research to be bought because otherwise XCom can't sanction their acquisition. Any case of looting and using these weapons before is considered "personal initiative" and since the Commander (player) is a no non-sense guy, he supports his agents doing what they need to do (especially since it's him who tells them what to do any ways) so it's a rare case of "turning a blind eye" but there can be no trace of XCom buying the weapon.
If anyone says: "LOL Why can't I buy an axe from day 1?!?! This is stooopid1!1!", the reason is the bureaucracy, already established as major in the story (ie it's the same as not being able to rent a van for 4 agents from day 1, etc.).
I believe this should take care of a decent part of it?
@Ragshak: There's no straightforward method for dealing with Assassins, it's the whole point of them. At least not in early game (yeah, thermal goggles will come later). If you suspect one's nearby, you should set a trap or something encircle him; at worst try to sacrifice only one person to draw them out. As Naruto taught us, ninja wars are brutal.
It would be nice if units on fire stopped being camouflaged. Then throwing an incendiary bomb could reveal enemies. I mean, if you're burning alive in a puddle of napalm, you're not going to manage staying still and hidden, are you? But only for enemies that are on fire (ie burning and losing health), just stepping in fire shouldn't do it.