One thing that is quite bothersome is how the various parameters configurable under the Options->Set menu are handled. It would really make sense for some of those parameters to be project-specific, the Drills in particular. The drill table changes across projects so, when used in conjunction with the drillegend-stack ULP (which requires the drills to be sorted by size), universally changing the drill table gets cumbersome. This is particularly onerous when switching between multiple projects, which I do frequently. Placing the drill table within the auspices of individual projects will keep them proper.
One other related suggestion would be a Sort button in the drill table dialog. I use drillegend-stack ULP to generate the drill table for my fabricator. Having to go in a manually sort the drill table is a manual task that should be readily automated.