to be helpful, one might suggest setting up a default project with commonly used instrument tracks already named and placed.
Actually I do have a few template projects, sequences, programs, pattern banks and pad assigns, but most of time I have to make changes to them and the naming issue comes up again

Another thing is that the more default files I create, the less default they become, too many...
I only wish I knew some of the basic programming involved with the JJOS so I could think of some improvements to the naming procedure that will take the least amount of work/time for JJ to implement.
I reckon that since there is already is a copy/paste function, the least programing way to go about this would be to expand this function. E.g. you could have the mpc copy a name to a pad. You would then have 64 copy/paste locations. It might work something like this:
1) Press copy and a window with 16 text fields comes up
2) Press the pad you want and the name is copied to that pad
---( you could have 4 banks with 16 name locations = 64 cells/names)
3) Press paste, the same window with 16 cells comes up
4) Hit the pad with the name you want and it gets pasted
5) The contents of the cells would be saved in the system steup file.
you get the idea....