I think the marker and cue point management is if I am honest a little clunky.

For starters I think you should be able to display cue points in a similar way to markers, which I notice other people have commented on.
The only difference would be a drop down box at the top which allowed you to select the track to specify which markers to display. This allows easier navigation through cue points, which currently seems tricky. I also find that it's quite easy to inadvertently pick up and move markers when navigating through the tracks and selecting regions etc. I think there should be an option to lock/unlock markers and cue points so their location can be fixed and locked when required avoiding such really annoying issues. Set, adjust, lock for example could be sequence when adding an important marker/cue point.