Deconstructing classes?

[Krieg]

Closest thing I've seen along this line is Joe Mucchiello's Character Customization, which I think I picked up at RPGNow. It's a .pdf file for designing classes & PrCs from the ground up, based on a lot of number crunching. At 75 pages, it covers a lot of contingencies.

There are two reviews of Character Customization on ENWorld's review page.

There was also a freebie PDF entitled "The Custom Hero" that was available at one point. The author, Leroy Van Camp III pulled it down when he decided to do a commercial version of the project, but I have no idea whatever happened with it.

 

[Caliber]

Here is a system created by Seasong, http://seasong.home.texas.net/sh/rules_class.html .

It involves some hefty changes to magic, however, and might need some modding if you want to use standard magic in it.