Currently you can only set up to 5 unit/structure hotkeys as comm, which is pretty disappointing to me. Here's some improvements that could be made:
Improve Grouped Unit Interface: Currently, you have to manually go into each unit in a group if you want it to perform certain actions (root and unroot for whips doesn't work for groups, but attack works oddly). You also can't cycle through the members of the group to easily perform actions by clicking on their icons at the bottom of the screen.
Increase the Amount of Keys that are Usable for Hotkeys: Speaks for itself pretty much. You can only set up to 5 groups/units to the 1-5 keys. I would like to see this improve to possibly the number pad keys and the rest of the number keys. That would give plenty of keys for us to use.
Make a Zoom to Key: It's really annoying trying to get around the map sometimes. It would be really nifty if we could set zoom waypoints that we could assign to hotkeys and a zoom to current unit button so we could zoom to whatever we have selected.
Improve the keyboard based movement system: It's rather annoying to have to use the mouse to scroll everywhere, even more so that the current system is based on using the arrow keys. These keys just need to be reassignable and they would be perfect. Personally, I'd like them to be assigned to WASD+Shift.
Those are some of the things I would really like to be put into the commander experience that could make it a lot better. People don't know about some of these hotkeys as well because they're not easily apparent on the UI or rebindable in the interface menu.