i wouldn't set it in the Sol system for starters, we're not invading earth, we're fighting a galactic war for the survival of life as we know it, Earth is merely one campaign..
put yourself in the alien mindset.
who are we?
the way i see it, the aliens are an alliance of various galactic powers working together.
why are we allied with each other?
i suggest a common threat, something that affects everyone equally. look at mass effect for a clear cut example of this: once the galaxy accepts the existence of the Reapers, small conflicts cease. differences are set aside to focus on a common foe, one that threatens everyone equally.
what are we doing?
the aliens are here to conquer Earth, but to what end? Earth is merely one of many battles being fought for control of precious resources. resources the alien alliance NEEDS to fight the much larger war.
it could even be inferred that the aliens are here to save us from a danger beyond our comprehension, and communications broke down somewhere along the line.
I always Imagined that the aliens were subservient to the etherials, in some sort of either conquered/uplifted or genetically engineered (sectoids) fashion. That said the point seems to be supported in the later games(especially if you consider interseptor cannon) and UFO itself from the various unlockable ufopedia entries. The uplift/aid of the human race would be too a nono, as seen both in the end if you lose the war in UFO, TFTD and again the other games of the series.
I always viewd humanity in the x-com world as an alien experiment gonne beyond its intended purpose:
The alien brain tells you that humanity is a byproduct from a race of martians and could have been an evolutionary mistake, been born by the accident of T'leth leaving the earth for millions of years without alien 'attendance'. That said the first documented contact according to cannon was in 1940something. The invasion begins in 1998. To my mind the Etherials somehow subjucated or created the other alien species, particylary the sectoids*, to serve as their tools.
Humanity (or whatever they planed to do) was another of those tools. But something gonne awefully wrong (T'leth been one of those things that went wrong) and left the planet to evolve on its own. Given the fact that both the UFO and TFD aliens are launching research missions to find out about the planet itself, I believe the theory of: "What the hell happened to this planet" is on an accurate course.
Again if you take Apocalypse and interceptor as cannon, there is a feeling that the aliens controll almost everything (At least in the neighbouring to earth star systems) but their civilisation is somehow decaying... and alliance suggested that they indeed are at war.
*The sectoids to me are the most high in the hierarchy after the Etherials been an engineered race and absolutely loyal to them. It appears they were given their own leeway to pursue things according to the alien agenda (T'leth was filled with sectoids and whatever the heck was C'thulu). However they seem to have their own ulterior motives as well (cross breeding etc)