I spent some time into an early UI, and plomped in some private (existing code) for plugin management and voila. Vista's glassy look really fits well here

It won't look as pretty on XP though. This shot should give you an idea of where I want to go.
On the left multiple sections to select from (treeview style), with on the right, the details to specify. In the top right you can pick your active profile to use (the combobox), and at the bottom a log window that will spew out details of what is done when the game is started/quitted (what you see there now is just some silly useless text but it's for the idea).
Please note that it's basically a mock-up and isn't really working yet. Any suggestions are welcome.
I'll try to start on a transactional management system that will track changes made to the game files in a couple of weeks. This will be the bulk of the work and may take quite some time. After that, it's time to actually start implementing 'real' features.
Here's the pic: