On Mac OS X it's only possible to start one instance of UPPAAL. At the same time UPPAAL only allows one project/system to be opened - opening a new system closes the currently opened system. This makes it impossible to have multiple systems opened at any given time - a real annoyance when, for instance, comparing two different systems.
A solution could either be to allow multiple windows to be opened with different systems, or to allow multiple systems in the Navigation Tree of the Editor view.
This has been a planned feature for ages and was relatively high on my personal wish list.