I heard a few fan theories besides the whole brood mother of race one, which I never believe because of her design.



1) Chrysalis isn't a pure breed changeling, she is a mule and one of her parents were a pony. Some say she is part unicorn others have said she is part alicorn, either because she was a lesser mule that ascending to hale alicorn or because one of her parents were an alicorn. Some have said that she either the alicorn sisters half-sister or their kid who has issues with her mother and aunt.



2) She is simply what a royal unreformed female changeling looks like much like how Thorax and Pharynx are what royal reformed male changelings look like, a royal reformed female changeling would look different.



3) The comic origin of changelings is canon and Chrysalis just took more after their pony side then the others did.



4) She is a mutant



5) The Love Poison theory which is the oldest theory: If you remember that season one episode the drawing of the princess that fell under the love poison was an alicorn, there are two different versions of this theory but they all go back to that drawing. The first being is that unknown alicorn and prince was Chrysalis parents and the changeling race started as the offspring of pony couples who were on the love poison, she only different because one of her parents were an alicorn while the normal changelings came about from normal ponies breeding while under the effects of the poison. The second version is that Chrysalis was that alicorn and the long term effects of the poison turn her into what she is now. The normal changelings started off as normal ponies who fell under the long term effects and just bred true.



I like number three the best just because I like the comics and think would be great to make more of them canon. But all of them has great story possibilities. I have to ask want you think of them.