I think the problem is that everyone has different ideas about the "best" layout of apps and data. Certainly, the Iyonix updater got a lot of flak in the early days because it assumed that you hadn't changed your HD layout. This only subsided when Castle enhanced it to seek out anything that had been moved.
I certainly like a mix of data held with apps and data held under subject-based directories - I doubt anyone else would like my scheme.
So I have to agree with John and others. Let us drag and drop the apps where we want them but help out with duplicated/wrong version/system resources etc.