I dunno, the alien plot in NewCOM 1 seems fine to me. But then, I don't assume that the aliens had limitless resources, or needed XCOM to win. I think they had limited but advanced resources, and just needed human DNA. But XCOM kicked their ass... Or, as it turns out, didn't.
Basically the Uber Ethereal was trying a desperate gambit. But not straight up lying - they did want us. They just didn't mean to wake us up (psionically) except in their labs.
* Abduct primitive hu-mans with expendable vat-grown scouts who still overcome all police and government forces.
* Oh what, this special forces team is confounding a portion of our efforts. Good thing all our weapons explode.
* Huh, lost some scout ships.
* ...They're doing *what* with the alloys? And they're figuring out elerium??
* Gloves come off, send in the cryssalids. The funding governments will collapse in anarchy. Loss of guinea pigs... unfortunate, but acceptable.
* Uh oh, that didn't work. Start mobilizing the honor guard (mutons) for ground assaults, rejects (floaters) first
* Uh oh, they found our base and *somehow reverse-engineered the key*. Commander down.
* Uh oh, the honor guard isn't stopping them, particularly since they've somehow reverse engineered our weapons. IN A CAVE! FROM SPARE PARTS!
* We'll just go down ourselves - Oh FUCK they're AWAKE
* And they built a bizarre McGuffin which beat our cloaking technology by hacking our psyberspace or some shit
* ... Maybe they'll negotiate?
* X_X
Is there a reason so many people seem sure that the EU aliens were "losing" on purpose?
I know Shen says it at one point... In like month two! He has no idea! All he knows is that their tech is strong, he has no idea what their resources are. And he's pretty much instantly proved wrong since the aliens begin total war through terror missions.
Of course the aliens could just orbitally bombard and "win", but:
1: The game is about ground tactics, air and space support are bizarrely lacking on both sides
2: Maybe they don't want to wreck the planet with all their precious samples on it.