Right now any character can learn and master any skill by whacking monsters. Which not only is unrealistic but also makes the game more boring, as the player can access his favourite skills with any character. So what I'm suggesting:

* Get rid of the skill selection screen during character creation. Initial skills should be determined by race and class, like in ADOM. This step just adds a couple of boring extra minutes to character creation, and the huge list might scare away newbies just wanting to try the game out. Character creation should be fast and easy.
* Make it so that skills at level 0 are disabled and cannot be raised nor used. When you level up and select skills to raise, hide all disabled skills - the shorter list should make leveling up less of an headache, as you don't have to worry about fifty of them anymore. As a way of learning new skills, their level could be raised above 0 as rewards from NPCs, like how you learn Courage from the old barbarian in ADOM.
* Make so that skills can be raised outside of gaining an experience level by training them (again, like in ADOM). In ADOM II mechanics, training a skill could lower the skill cost for the next skill level, and when the cost reaches 0, the skill would advance to the next level. That way, you learn by doing. Which is what most skill systems should be based on.