I'm still not sure, if the old solution was better than the new memory system. You needed more investment (skill points) to even learn higher level skills, now you need hardly any. Also now you need to use attribute points to use more skills instead of using skill points to do it, which would be still more logical?
You're talking about D:OS 1's ability point system, right?
I think that could be another part of the solution to too many known skills. Skills in D:OS 2 right now only need 1 point in the required ability. I think that it might be a good idea to partly go back there so higher power Skills need additional points in the required Ability.
Couple that idea with making Memory something you need to invest in and that should help with the problem of "know everything, do everything" characters.