It is common to have a recently opened files and be able to pin items on this list. Why not extend this idea to the JMP menu/toolbar items?
How about a sidebar (with oversize icons?) where 'favourite' menu/toolbar items appear and can be pinned. The number of items that appear on this list could also be customised.
I could create a favourites menu/toolbar manually but that would require keeping a mental note of which menu/toolbar items I use most. Being able to expose the usage statistics to the end user might also prove enlightening?