Numpad Doesn't work.
This may be a personal gripe of mine, but when I was using MS3, I would retool the keyboard shortcuts so that I wasn't typing all over the keyboard just to put in a few notes. They way I would do it is I would take all the notes and put them on the U, I, O, P, J, K, and L keys (since the QWERY/WASD keys were so heavily-used in other important shortcuts), and then use Shift and Ctrl to stack notes on the staff. Then I would put all the durations (e.g. quarter note, half note, etc.) on the numpad, with the note rest being the 0 key. However, in MS4, while the Numpad is accepted in terms of shortcut configuration, when you try to use them, nothing happens, mainly because, I believe, that while it accepted the information from those keys, it just interpreted as the regular number keys across the top of the keyboard. So they never work. I hope that makes sense.
It's really cumbersome to try to put in note durations, when I have to keep moving around all over the keyboard. I'd like them all in the same place for quick use, like I was able to do in MS3. It's just about the ONLY reason I don't use MS4 that much, add to it that the file format has changed so much MS3 can't read MS4 files.