Off the top of my head:
Bluetooth for mobile device app
USB host port for midi control or USB stick storage
Selectable output sample rate
I/O routing matrix
Treat CPU as a pooled resource so there are no limits on the number of each block type in a preset
A more flexible IR system that doesn't reference IR slot numbers in presets, thus making it possible to reorganize IRs
Bidirectional MIDI so controllers can reflect parameter values when a preset is loaded
Eliminate the constraint of a fixed number of columns in the grid
Sort out the distinction between block types and block presets in the type menus
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IMHO though, a key area that deserves attention is workflow: For one example, there's a whole host of things related to managing presets: Organize into folders, notes and comments, favorites, ratings, tags, similarity searching, searching on attributes of a preset, locking parts of a preset when browsing, boolean expressions, treat the computer as a storage location for the library of presets, etc.