Along with the a-synchronous topic that was brought up by Charlie, I would like the ability to keep a pattern playing wilst modifying the drum pattern, or another section real-time, and then having those changes effect the current audio at the user's will. It seems this would entail improvements to the sections/playlist functionality.
I would also like to see the pallets and various functionality encapsulated in collapsable windows such as Omni Group's omniGraffle. Otherwise, the velocity controls should be incorporated into the single window. The only window that I could see being a floater is the transport.