One thing I was thinking was that the plugin could include certain plugins and enter the licenses for them! Take for instance BackupBuddy and Gravity Forms. In my packaged array, I could enter the licenses for those licenses and the class would insert these into the appropriate places (providing appropriate filters/hooks to extend), that would be awesome (yet difficult).
I like the idea. I'll slate it for 3.0.0 and have Gary weigh in on it as well.
I don't like this idea.
Let's consider some scenarios:
1) You're a developer creating a theme to sell. It's unlikely you'd want to be including your premium plugin license key with every sale, even if the plugin license conditions did allow you to give it away and be used on sites that are not yours.
2) You're a developer creating a theme for a particular client. Presumably when you copy the theme files across, you have FTP access and can install whatever plugins and set them up as needed - TGMPA isn't really useful for this case.
Most plugins don't need license keys, so I can't see how this addition would benefit 80% of TGMPA users - by all means @wpsmith consider how you might do this as an addition class or two for TGMPA, and if you need a hook added to the TGMPA core for it to work, we can probably add it, but I don't think it should be something going into core.