There have been so many suggestions about colouring them, placing them in a tree layout to make finding specific BM's easier. If they've done nothing to even help with this situation, it shows they are going down their own route and little or nothing suggested by the players is even being considered. At present, you have a list of BM's as long as your arm and no way to organise them to make them easier to find, even without increasing the number. While I understand you dilemma about the number of BM's we can have, without some sort of way to order them, increasing the amount would only serve to make an even longer list to scroll down.
As a programmer myself, I know that creating an folder system for them wouldn't involve too much work really.
Not sure how the interface handles coloured text so I can't say too much about having player designated colours for them though. Considering how many lines need to be changed in order to simply change the base UI colour, I'd say the colour system was a little too complex for what it achieves, but that complexity could be useful in achieving other things as well. Not sure if it was designed with that in mind, (considering FD don't seem to be very forthcoming with their ideas for the future of the game).