Sub folders 100%
Global midi channel setting
Agreed that mono/stereo settings would be nice.
Maybe this is already a possibility but USB audio interface integration
I think the multiple patch idea could be possible now. It would have to be able to access the folder containing all patches and allow you to select multiple. If a "root" patch could be loaded which utilized the menu knob to navigate you could select patches to run. Use the menu to swap out patches for others exit back to the main menu, save preset combinations. Even split the keyboard, although a "note in $0" type object (or something like that, I still don't fully grasp those) Would be needed to give each sub patch a unique ID.
As for knob glitchiness, you can do a lot with pd to filter that. I have used sub patches to turn the 0-1 value into 128 discreet values with some simple math and a change object to stop any duplicate bangs. Fwiw.