Martin, you're absolutely right that there are many uses to controlling all sorts of parameters with functions or other shaders, and we have this marked for future development. There are some things that won't give the results you expect, though. If you've tried to use the 'scale' input on the Perlin 3D Scalar function or the voronoi functions, you might have noticed that changing the scale has weird effects because it distorts the domain rather than changing the size of individual features. Either we just accept those limitations, or these cases need some special care on our end to make them usable. Another side of this is that there are plenty of things where we would have to reengineer the shaders to make every parameter pluggable, in a way that would make them less efficient. These things are possible but we're not attempting them just yet. In certain cases, such as the Cloud Layer, we identified particular needs/requests and came up with a solution for them, and we'll probably keep doing that on certain nodes as part of ongoing development. The specific case of modulating the size of the stones in the Fake Stones Shader is also something I've thought about. I'm also interested in making it produce a range of different sizes within one node, and after something like that is working it would be relatively easy to make the size controllable with another input. Sadly that's not something we're planning to do soon, because we have some pretty big projects we need to concentrate on in 2012.
Chris, the idea of modulating the settings on the Alpine Fractal Shader came up before and I'm keen on making that more pluggable in future.