Prestige Classes [3.5/E6]

Recently I've been playing with the idea of using the E6 variant for my D&D campaigns. I like the variant because it limits the power of casters and keeps magic scare in the world (something that generally helps balance and also leads to worlds that I like working with.)

However, there seems to be one flaw with the system: Prestige classing is almost impossible. Most characters only get to the point where they could have one level of a prestige class working with 3.5. There seem to be two solutions to this: First lower the requirements for prestige classes, allowing characters to access them by 4th or 5th level, thus allowing more development in them. The second option is to tweak prestige classes and use them as base classes.

I'm personally leaning towards the second, but even with only a few prestige classes, I'm worried that all of the new base classes (which would be pseudo variants of the 12 core base classes) would make things too clunky. Perhaps they could be better replaced by archetypes like Pathfinder uses or by feat trees.
Any opinions welcome.

The feat tree possibility seems the easiest solution to me. Since the E6 variant is made with the idea that you simply gain additional feats instead of leveling up after 6th level, making feats which allow you to essentially create yourself a role seems a pretty good idea.

Alternately, you could design 1-level variants to popular prestige classes that grant the most iconic power of the class (without regard to whether it's normally granted at the 1st level of the class). Providing secondary features through feat support would also be compatible with this approach.