TFTD didn't happen in this storyline. The diverging point is around 1999-20xx, depending on when the invasion happened. The human civilization didn't grind to halt overnight, too, it took several generations, the Empire wasn't in a haste, hence things like UAC weapons. However, the TFTD aliens have awakened, stirred by long and heavy rain of hyperwave chatter that began after the invasion. When? Nobody's sure, they didn't act hastily. The massive Deep One (I know they're called Gillmen, but I've decided for the original Lovecraftian name) invasion is comparatively recent, maybe a 100 years back or less.
The earth of 2600 has maybe a couple tens of millions purebloods left, and at least 10-20 times more mutants. A large lot of them is near-baseline though and generally accepted by most humans - but not by the Humanists who are extremists. But then again, whole Piratez Earth is what we would call a "revolting alien experiment", and for a good reason. But then again, it was the Star Gods who raised the man from the ape, according to XCom lore..
The Uber strain is indeed psi-weaker than Ethereals, but on the other hand, never as weak as some humans are. 10-15% of wild humans were psi-stronger than (probably) any Ethereal... But those humans are basically long dead, targeted by Ethereal bio-weapons and hunted down almost to the last. 2600's Humans Psi Str caps at about 65 (with very rare exceptions), and ALL their physical stats are inferior to the Uber strain. Sure, a very-well trained human would be superior to most of your starting recruits, but - basically no further advancement.
The Pirate gals also do not employ Sectoid hybrids, as even the strongest of bug-eyes would be only somewhat stronger than the strongest of the uber strain, while being pathetic physically. Sectoids cannot match Ethereals, their hybrids neither, they learn psi very fast but I think their capacity would be capped at around 70 Psi Str/70 Skill. They do face discrimination, because the psi comes natural to them - they do not need any lessons to have Psi Skill, they don't need Psi Amps to use their powers either, and these things scare people - not only purebloods, but most non-psionic mutants as well. And fear leads to aggression. The ubers thus might like bug-eyes as their fellow mutant brethren... but only from afar. Ubers are prideful and as prone to chauvinism as the pureblood humans are - after all, they have named themselves "the Ubers"
As for the Sectoids and their own hybrid line - wait till this part of the story is introduced... There will be Sectoids (and Aquatoids).
