I found the less I used submenus, the faster everything goes. Everything on the phone, I mean, or at least what I do. I was running into system apps force close/wait pop ups, I think because I had too much running at once, and when I emptied my subdirectories, those things seemed to have subsided and lag has decreased. I've only been in this configuration for a few minutes.
I do think this is a fantastic and much-needed endeavor, but since it's really so fundamenal to the system (runs all the time, gets used a lot, gets used when people are in a hurry) and seems very complex, it's very ambitious.
So far I seem to be running well just having all my games (too many) in a folder, which cuts down on the app drawer clutter a lot, and one folder of less used shortcuts (settings for specific apps, volume tweaker), but if I start organizing too much more than that, things start to slow down and get buggy.
It's not worth its own post, but I'd love to be able to rename my subdirectories.