What makes limited skills a rather big issue is that the game has these four skill types
1) Useless over time
2) Useless within builds
3) Useless once you got better
4) Useless except in one situation

-Fortify starts off useful (less so in EE) but ends up being a waste of a slot (and honestly THERE IS NO reason it should be useless... Why doesn't this scale?)
-Lightning Jump can be outright detrimental for certain builds
-Skeleton Warrior is an inferior version of a later summon that far outclasses it
-Wolf is a summon for Hyberium and is completely useless as soon as your done

Now... With limit skills these are an issue. With the potential for unlimited learning it isn't. You shouldn't need to memorize what skills are useful later to be competent with the game.

I agree with the idea that mastery should give unlimited skills to be learned but should have to be slotted to be used BETWEEN battles or checkpoints or some other manner.