Recently I got a rejection notice and one of the items was the Validation Team (Test Team) tried to double click on the main jar of my java app and expected it to launch and run. It runs fine in Appup is what they said but double clicking the jar in a folder launched but it did not work.
When I resubmitted I said please do not try that since you need to be an appup engineer to figure out how they launched it correctly considering how Appup works. If you want to launch any java app outside of appup I am guessing the appup engineers launched it knowing the correct jvm to use (path to it) and any command line parameters including a java policy file). The reason for all that is there may be a 64-bit jvm installed and if there is a 32-bit one (enforced by appup) and depending upon install order it may launch the app but not work properly at all.
Ok someone may say does not 32-bit java apps work with a 64-bit jvm? The answer is no especially when you use jogl for gaming and other frameworks for special things like video and 3-D mapping because there may only be support for 32-bit java still.
So please do not go outside of Appup since the engineers of Appup worked really hard to get apps to work inside of it for lots of reasons and if you go outside you are probably going to not have it work.
If you want apps for appup to work outside of it the testers should make an enhancement request of Appup Engineering and have the install create a proper shortcut on the windows desktop that points to the proper jre, startup command line params at a minimum and whatever else Appup requires.