Cool idea.
I was thinking, but not yet tested, that the greater differences between classes could come from the runes cost for each skill and the runes gained each level.
This will pre-derteminate the choices you make when leveling up but at the same time allow everyone to try different tactics. This idea is best designed in this game:
http://www.pathofexile.com/passive-skill-tree
Where all skills are available for every class but if a warrior wants to cast spells has to pay much more to do so. Each class starts at a different position on the skill tree and some skills are closer some are very far away and you need many steps to reach them.