What I would really like to see is that at least all the Marshalls and Fenders are together in the list order instead of being all over. For example, all the Marshalls could start w/ "Brit" instead of some Brit, some Plexi, some JM or JS, and some start w/ the model #. All Fenders could start with "Cal" or "F" or something. This would make it a lot easier to quickly select different models to compare instead of having to scroll (especially on the hardware).
If the models were grouped into submenus, the way that would make sense to me would be to group them by the channels available on the actual physical amp. So for example, all the channels of the Hook go into a submenu under Hook; the normal/bright/jump channels of a plexi go under Plexi 100, the 3 Triptik models go together, the Normal and Vibrato channels of the Deluxe (or Twin), etc. This should make sense to anyone coming to the AFX.
Anything that involves individual intepretation - what's clean, what's low gain, what's high gain, etc - could be handled by each person with their own custom tags. Ideal would be to have multiple tags so you could put an amp into more than one category if you wanted.