Lol, so this whole time I've been bouncing tracks and thinking I can only have the plugin active on a single track at once??
What I think would be good is to have a main window. Every time, you open another instance of a Melodyne plug-in, it opens in that window. The data will squeeze together a lot tighter because you don't have to repeat all the regular info and you can get more tracks on your screen.
Also, you won't have to drag windows around, putting them right underneath each other - they will already be in alignment. This way you can work with harmonies because you can easily see the original melody.