How about punish training in only three skills more so that we dont get those monsters that no one want and no one can afford except the NT that does not have to pay his salary?
There is no reason to add new penalty. High salary for mutants is enough penalty.
Moreover mutants aren't big problem. In past I remember few players with salary over 600k. Currently in whole game we have only 4 players with salary over 400k, and I'm sure, that in next season this number will be smaller.
Of course these players were needed in past because before they were created we didn't know how formula of salary works or if it's possible to cap ATG player. Thanks these players our knowledge about game is better. And it looks that system works very well because number of mutants systematically decreases. It's evolution, we don't need revolution. Darwin's theory is valid in BB too. IRL mutants died without salary cap.
Additionaly we have elastic effect which makes creating of mutants less effective.
And one more thing. I can imagine player with 3 skills >= 20, all other skills not higher than 10, and salary not higher than 150-200k, who will be worth fortune for all teams in top-32 of B3. So training only 3 skills isn't problem too.