From Star Control..
A few things, the aliens coming after our world, probably would have some enemies of their own.
Having a few "converted" aliens, or alien verse alien violence as a playable character would be useful.
As well as the easy to use Alien artifact upgrades to weaponary and stats.
For example, in star control, you can add more crew to a ship if your found a precursor object.
This can be added to X-com on certain missions that could point to an alien technology or be utilitzed for alien technology.
Maximum 60 rounds of ammunition to say a machine gun.. improvements via another alien technology
may allow for 100 rounds of ammo per clip, or new kind of rounds of ammuntion. if you stop to think
about it, why didn't X-com develop new kinds of armor piercing ammo made out of alien material?
Others could be direct interrogations with the aliens, as a storyline side feature for dealing with alien races.
If not the hundreds of weapons ideas from star control, how about a cloaked alien, or an alien with a power shield that
is rendered bulletproof etc..