Perhaps the ship has already sailed, and everyone has a million suggestions here already.

I would like to suggest the screen displaying 1 larger racial tree (as it is now), but then six smaller trees that could fit over the current real estate of the three class trees. Each class tree can be cut in half by creating a "general" class tree that can hold all of those things that every cleric or ranger or arti should have. Favored enemy, rune arm charging, and pet enhancements are those that come to mind of the top of my head. The point requirements of the prestige trees can be satisfied by taking points from the general tree.

So in summary, 1 racial tree + 6 smaller class trees would give a lot more flexibility to the system.