this is well beyond V1.0, but perhaps something worth looking into, as it goes beyond anything a mod can easily achieve but might improve gameplay...
I suggest you make the craft weapon icons in the interception screen clickable to temporarily switch them off.
especially in the early game you quickly realise that the small scout ufos will be destroyed by a missile hit. so if you actually want to shoot them down to capture that single alien (or at least kill it and take its weapons) instead of blowing it into oblivion, you have to send a cannon-only craft after it.
having one of those is a waste of a perfectly good craft that could be used for other purposes, too.
if, on the other hand, you always equip your crafts with the best weapons available, and are meticulous about shooting down every ufo you find, you will end up wasting lots of expensive avalanche missiles for tiny ufos you could also destroy with a stingray
a stingray which will however only be fired after the avalanche missile has already been fired. so most of the time you end up using two missiles on a tiny ufo.
later in the game, you might have an avenger with a plasma cannon and a fusion ball launcher. again, you will end up destroying lots of smaller ufos unintendedly while wasting fusion shots you might need for a larger ufo that pops up after you shot down the first one.
the simple solution would be to allow the player to temporarily disable one (or both, if you're suicidal) of the crafts weapons. you might even turn this into its own gameplay element: if your craft is fast enough, you could script a forced landing of the ufo that happens when your craft reaches the UFO in the interception screen. so you have the option to "run it down" instead of shooting it down - which would only be possible by switching off your weapons.
this would also make the firestorm a good deal more valuable again, since it's the fastest craft out there. who cares that it only has one weapon: it could run down larger UFOs, allowing your troops to capture them on the ground.
what do you think?