This was actually one of the biggest challenge I had when I was making my LQGR - OMG maps.
The way Combo color works is with a flag, which is 1 or 5 for hitcircles (1 being keep same color, 5 is go to next color), and for sliders, its 2 and 6. I'd actually be interested to know why it was made like this, but anyways.
Point is, I think it would be better if you could choose a number between 1 and 5 (which corresponds to the combo color #), and each of them is the specific color. Of course, by default, the in-game editor would be almost similar, with the only difference that you can keep on hitting new combo color to swap through the 5 different colors.
But I'd understand that backward compability could be a big issue here.
EDIT: fff I didn't read the entire thread, oh well I think mine is pretty similar to MM's, but more with the actual .osu code.