So I don't really think she's trying to breed a strong superhuman for her to consume later on. Unless she's completely unaware of the risks, I don't really see her being dumb enough to attempt something so dangerous.
On a similar note, I don't think the MC will be able to kill Jake in a traditional sense if it comes to that, I'm going out on a whim and saying that his powers will give him an advantage in the aforementioned mental battle.
I dont kill girls i want in my harem, so i dont know what you were talking about before, but i think ella knows the risks pretty well and has higher goals...much higher goals. We saw 3 evolutions, 2 own and jakes in the end, they all have mental messages in foreign language in common, we even saw a vision of "mother"...i think that all evolutions are pretty similar, fragments of memory, maybe even some hive mind that connects you with the monsters you see in your dreams. We learned the source is or was on the moon. So it could be everything between an invasion and an emergency call...
We know for sure ella is more evolved, maybe she understands the message/language already, is remotely controlled by "mother" to spread the infection or want to overpower and absorb her/it...or its even simpler, she could have been a testsubject by doc xanthe herself and wants revenge, but is to weak to break through his guards...this would allow both ways, absorbing powers or forming an army.
If i remember correctly you can absorb dead people as well...so it would be easy to kill him first and absorb his dna, memory and skills then...it didnt work with kenny because he was like ella said a failure, you could do it anyway, but then you get the dead end because you lose your mind too, but it should work with a more or less sane victim...and we are still a evolution step ahead him.