Here is a proposal for the Skill System:
I would propose to invent some class-exclusive skills. Skills which only certain character classes or races can use.
In 3.5 the problem was solved with cross-classed skills or feats (tracking). Or you had a special text in the skilldescription that you only can use it if you have a special class (e.g. magic traps). Disadvantage is that there is an unbalanced number of skillpoints.
It would give the game some nice new character options:
What about:
Exclusice Rogue Skills:
Disarm magic traps
Pick locks
Critical hit chance
Exclusive Ranger Skills:
Tracking
Exclusive Mage Skills:
Ancient Arcana
Exclusive Bard Skills:
Bard Song
etc.
