I'd like at a minimum control over line thickness of the data plots. I often use data from the saleae in presentations, and having control over theme settings would make screenshots more useable and cut down on the work I need to do to get the data ready to present. It would also allow me to show live data capture, and actually have the audience see the results of a demo.
Settings would include (but not limited to):
Line color, thickness, and style (dashed, solid, etc)
Fonts (separate fonts for labels, axes, etc.) (Color, size, typeface, etc.)
All of these are currently coded into the UI in some way. If you can extract these settings to a file, that would be a start. Adding a gui to make all the adjustments could come later.