3.0 (and 3.5) are pretty cohesive systems. There are a lot of parts that, if changed in a significant way, require that other parts of the system be changed significantly as well. But that doesn't prohibit you from changing them.
Me, I like the rules as written. Generally play by 'em. As they say, "if it ain't broke, don't fix it." But there's also stuff I don't like. But in that instance I tend to ignore rules rather than write new ones.