I have several gripes about the current DP6 GUI. The double title bars on the windows (the narrow one on top, and the larger one with the gradient below it) are really lame. It makes things very cluttered and visually confusing, especially when you have multiple overlapping windows (and no, consolidated windows is not always the solution!).
Then there's the event data that's displayed at the top of editing windows -- it's a big long line of numbers with no indication of what they mean. Every time I try to find a note-on velocity or a volume value it's a big pain to hunt for the correct field in that huge line of stuff.
A lot of the graphic elements are poorly designed, like the vertical slider that scrolls MIDI notes in the sequence window -- it's absurdly narrow. The Track Groups window has buttons to turn on and off various track groups, but the state indication is either white or light gray -- every time I look at this I have to ponder which color is on/off. Seriously MOTU, how about a big fat CHECKMARK in the box, or a nice bright GREEN SQUARE to indicate an active group?
