i think their should be a lot more weapons, especially on earths side, civilian designed technology that isnt just for aliens, more improved conventianal guns, like gattling guns, setable charges, put that anti alian gas into the grenade launcher, make other things like the machine gun with built in under grenade launcher, 1 shot weapon. proximity charges. your using the quake engine so perhaps enable shadows and include flashlights, flairs, IR vision, placable camera's, give people an engineering skill to set up things like trip wires, placable cameras, proximity grenades, land mines, mine detectors.
why not go the whole hog, and have civilian vehicles you can comandeer, motorcycles, cars, jeeps, tanks, much like the HWP in Xcom.
Why do aliens have to attack just your bases, what about other countries military bases. civilians dont have to be defenceless, why not get them to have shotties, pistols and shoot at you as well, coz their scared, wounded etc as well as trained soldiers of other countries.
have defencive weapons on your aircraft, requires somebody to operate it, some of those transport ships do have weapons, could be very leathal and provide cover for troops disembarking from the ship. vise versa too with alien ships.
as for armour, should have various parts of it, vest, helmet, gloves, boots, have power armour like robot suits, suits with breathing aparatus's, flame resistant, dive suits, shadow suits, reflective invisibility suits, flying suits. space suit, and have different versions of it, like you can make a dive suit, then an armoured dive suit, then a flying dive suit, then do the same for space suits etc, these would obviously be too heavy to use on land.
why limit your self to land, have sea based and space based missions, that require different air air crafts, armour as above to suit.
always have land and sea based attacks instead of flying their ;-)
my 2 cents anyway