Just a little thing that would somehow make the application more intuitive (for me) - for all windows, Esc closes the current window, except the main window. If the main window is set to dock in the system tray, Esc pops it back there.
In addition, WebIssues is replacing (for many things) Keynote for me (link), which provides a global (system-wide) hot key to bring the app back up from the system tray. Replicating that would also be terrific.
I can probably create this behaviour with a third-party "hot key binder", but think it would be terrific to have this integrated.