Hmmmmmm,
Well, let me tackle this post one point at a time. About the skills and spells, just as in real life, there is only so much one can learn from a book and an instructor. It is a case of "practise makes perfect", which means that through repeated usage, it not only leads to being used with more ease through familiarity, but you will discover some extra little things you will improve upon to make it the more powerful and effective. Why should such be any different in a MUD? And the effects are already in play, anything else would be superfluous.
As for the argument about augments not being as good, look at it in this light.....it would be like an aeronautics mechanic learning at the mid-way point of their vocation how to repair auto engines. Yes, they can do the repairs, but they will never be as good as someone that was, for all intents and purposes, "born" to do the same. You cannot expect a gladiator to be all of a sudden able to gate to the GMA or Arthenon and be able to rival A mage tier in casting of nova, nor an Archwizard to be a master of the sword, nor a rogue to be an expert in woodlore. It isn't realistic, for lack of a better term.
I think the way the system is, as it stands is fine.