Looking at your original post ive decided to actually try to animate something which vaguely imitates your original idea:
you can probably already see the similarities to the evolution tree in ancestors.
i can see how your specialization is quite different from a skill tree. however linear progression is inevitable or rather. It would be inevitable for the evolution of certain things such as the nucleus.
ive tried my best to make this animation show the possibility’s and show how not everything would be linear by taking some liberties. the locked primary evolution points (the big cyan circles with holes inside them) are locked. which when unlocked would display more secondary evolution points. (the dark gray points with lines connecting them) These primary evolution points could be unlocked through certain events like endosymbiosis. and unlocked with them would be secondary evolution points which grants specialization.
that was probably quite hard to understand so allow me to paraphrase by giving an example
Lets say we undergo endosymbiosis and engulf a mitochondrion like cell. This would unlock a Primary evolution point (P.E.P) and allow for us to specialize this mitochondrion symbiant. (seen here through the gray secondary evolution point)
by unlocking and evolving one of these specialization you would lock the other secondary evolution point, thus reducing overpowered and glutton cells.
I think @TJwhale made some solid points when he talked about commitment to a certain playstyles after investing many mutation points. which is why i made the decision to implement numerous Primary Evolution points with short branches which would make re-specialization much easier.