Hey Hazzmat,
We wanted to include the old leveling system (The meditation menu was more of an emergency solution), but the problem was that you couldn't add new perk trees or remove old ones in the leveling system. And, even worse, I believe the perk menu was hardcoded, so we couldn't even edit in Flash. There were attempts to hard-code a new menu similar to the hero menu, but we dropped these plans because we didn't have enough manpower. Maybe someone skilled in Flash will implement an alternative leveling menu eventually - if that's the case we'd be happy to merge it with the original game.
In other words: I fully agree. While it looks cool to begin with, it gets somewhat of a chore eventually.