I think it would be nice to have context applied to certain actions. For example if you have the Fill Tool selected, I could press ‘A’ to toggle “Contiguous”. But in the current state, the ‘A’ key is now no longer available to do anything else, and it only functions when the Fill Tool is selected. It would be nice if there were some check boxes, at least for the tools to say “while x tool is active” press ‘A’ to do y action, rather than setting all hotkeys globally (with the exception of currently specified hotkeys).
Also another feature that I would really like to see is the ability to have right-click be set to “Pick foreground color” while having right-click and drag be “Rectangular Marquee”. It was the system they used in Graphics Gale and it was intuitive and really sped up my work flow.