B: Point-dependent Skills: The greatest example here is Linguistics. For every point, one gains a language. Under this system, there will be no in-built way to learn languages other than by the Retraining System of learning languages by spending time on them.
This is a problem only in Linguistics and Performance adding in per rank specializations (individual languages or instruments/performance types) and requiring a new way of handling that. Many (myself included) would see breaking this link of "I get a skill rank I learn a new language" as a feature rather than a problem. The retraining rules appear adequate for languages and could be adapted to performance. Traits would also be good here. I'm hesitant on feats for this as there they could be seen as burned feats that could be better spent on something less situational and with more mechanical impact (especially in combat).