There are many X-com like games. And all of them give the answer to the question: why are the aliens attacking earth?
Energy/mineral resources? - interstellar species do not need to fight over resources - there whole galaxy full of uninhabited star systems.
Genetic material? Why do you need to fly so far when you can spend less time and resources making research using your own genetic material.
And fully developed interstellar race will have the power to wipe out entire humanity without much effort. Why terror tactic by foot soldiers? Why not the orbital bombardment by giant space battleships?
So i suggest some different view:
All different alien races flee from more powerful and advanced civilization. This civilization (Great Enemy) destroyed their empires. Remnants of refugee fleets come to the solar system as they seek to hide from their enemy in uncharted region of space.
Alien races come as few dominant races with their thrall races.
- Technologically advanced race group – with better weapons but no psionic abilities. This race will rely on tech.
- Psionically advanced race group – with powerful psionic abilities and medium tech. This race will rely on biology/Psionics
- Biology-oriented race-swarm (like zerg or tyranids) with big groups of weak units, strong officers but only medium tech/abilities. This race will rely on biology/numbers
All these race groups have few unique technologies to research. Also leading race units will be fewer in numbers but stronger then thrall races units.
These races seek to dominate Earth to survive, and form the fragile alliance. With only several damaged transport and military ships, they cannot conquer Earth in direct military operation, so they use raids and terror attacks to seed chaos and then to take control by forcing governments to surrender. Then they plan to enslave the population and establish the base to rebuild their strength, and make an outpost from which to begin to rebuild their empires.
Aliens can build their bases on earth surface (or deep in the ocean depths), but their main bases are separate and not accessible by human technologies (Moon or Mars base, damaged mothership in space, etc).
To defeat the aliens all of their main bases must be destroyed. To access main alien base all unique technologies for that race must be researched (for example: for tech race friend or foe identification device must be obtained and reprogrammed to open their base) and some spacecraft to deliver strike team must be built.
There are also can be story missions to destroy/defeat thrall races. For example: destroying the factory where Androns being produced will severely reduce their numbers in missions or end their appearance in the game.
All leader races will have one or two unique ufos, but other ufos will be the same for all races, constructed in the solar system specifically for invasion on Earth.
Governments/regions on Earth can surrender to one leading alien race, and will be freed when this race will be defeated.
This can be done without big changes in game mechanics.
But more units/races can be added. Fro example:
After some time when some Government/region surrendered to the alien race, there can be appearance of modified human soldiers fighting on alien side. For each leading race there will be different type of human soldier: cybernetically enhanced, mind controlled and genetically modified. There can be technologies to better fight these enemies, or to enhance player soldiers in similar way. To free Government/region from alien control there will be mission to destroy alien base on this territory. This base will contain at least one leader race commander (governor), his alien bodyguards, and some number of modified soldiers.
Or there can be appearance of the Great Enemy units in the game. Great Enemy will fight the other aliens but will not try to conquer Earth, because we are too primitive for them to waste time on us. These aliens will be very few and extremely difficult to kill, but their tech will be more advanced then anything else. For example: in the mission there are downed UFO and several dead aliens on the map, some living aliens who will attack player soldiers, and one or two Great Enemy units, who will attack both aliens and humans. Great Enemy units can use stealth tech like the Predators or just be the tanks with a lot of armor and heavy weapons. This units must be strong enough to single-handedly wipe other aliens and player squad. Their tech is to complex to be understood and to be replicated by the other aliens or humans, but trophies (weapons, artifacts) can be used by human soldiers.
There will be no Great Enemy bases and they will leave the solar system after all other races will be destroyed. Or their base will be the last base to destroy.