Looking through the Dungeons and Dragons core books, they have a great list of "feats" that you can select (one every three levels, more for Humans, Fighters and Wizards). A number of feats require other feats be purchased first and tend to be more of a level increase than a new skill. The feat-trees in D&D involve, at most, 5 or 6 feats, just enough to prevent a player being over powered at low levels.
Another idea I had is minimum attribute requirements for skills. For example, a Wizard with a Strength of 10 should not be able to have level 5 Stun. Some skills should have a requirement Strength 15/30/45/60/75 (for each level) rather than a character level requirement.
