Firaxis or whoever owns the IP could make a game where the Chosen rebelled against their masters. Maybe they allied with another alien race [or maybe just a small group of survivors of another alien race]
They could even leverage their old IP by making the original game a lead-in.
So you beat the aliens on earth, and then all of a sudden a friendlier/prettier version of the Chosen appear. [C'mon don't tell me none of you have considered a roll in the hay with the assassin, even though her grill is busted]
They explain that they broke out of the cloning cycle years ago and they actually helped create the conditions to allow the commander to be rescued. They didn't make it easy though, because they had their own problems.
And some steampunk reptilian mercenaries actually came in and helped. They were the species that was the basis for the Serpent/Thin Men. They are actually bipedal. The aliens dominated their planet when they were in a "Victorian" era, except they understood gravity so they had the equivalent of 18'th century lamp-posts but also floating cities and airships.
Very few of them survived, and they followed the enemy to Earth and set up a colony nearby to figure out how to defeat the aliens.
Xcom2 - The Chosen is just the Human's part of emancipating themselves from the enemy.
Xcom3 - Rebirth is the Chosen and allies from other defeated species and how they ultimately defeat the 4th dimensional scientists
"The Chosen" are unique because they are genetically created from an amalgamation of other conquered species.