1.) current constant colors are done by integers, but it seems that flot's default array of colors is only five colors long, and then it starts darkening/brightening. I think we might be better served by having explicitly declared colors, chosen so that sets of things that go together have neatly distinct colors (while less-common combinations may have less-distinct colors). My plan is to ask someone with better color sense than me (Batsy, probably) for advice, after I've figured out what all the categories are, i.e., which lines go with which other lines.
2.) Once that's done, we have straight hex values for all the colors (rather than flot generating them from its magical array and darkening/lightening procedure) so we can turn off flot's autogenerated legend, move up the checkboxes, and add the colors to that (perhaps only for enabled lines, the rest perhaps are just grey), thus combining the legend and the checkboxes.