I'm no math geek, but I do see the problem. This is the problem:
Even though I have only being playing pure builds, I can see where this will be a problem with multi-classing. And I'm fearing it might even affect the pure class builds by forcing players into a Prestige class they don't want because the enhancements that I want are stuck in the "most appropriate" prestige class tree, for example all sneak attack damage being shoved into Assassin, so even if you don't max out sneak attack you'll still get a large portion of the Assassin enhancements thus forcing people who want Acrobats and Mechanics into an Assassin build (yet again).
I'm going to have to go back to my original statement that this tree system might not even be necessary and just tinkering with a system that works except for the collapsed enhancements resetting every time something is selected. As things look now, this new system is going to limit builds (some severely some moderately) which won't make several players happy since its locking options out and preventing true customization.