There are builds for jailbroken and non-jailbroken devices.
On non-jailbroken devices you must resign the app bundle with your own Apple developer certificate.
Changelog:
Added native l2cap bluetooth support for up to 4 PS3 Sixaxis controllers (you must store the Bluetooth address of your iOS device in your controller with a 3rd party utility like SixaxisPairTool)... (Only jailbroken builds)
Added touch button and touch stick size selectors.
Fixed permissions errors when creating files on jailbroken devices.
Bluetooth manager bug fixes. (Only jailbroken builds)
Because some of the apps will get broken. This why I don't do it on mine. Unless I get a new iPad then I will do it on the old one. Have you seen all the reports on the iTunes? Some of the people reporting some of the apps doesn't work right. That because they are using Jailbroken. I rather stick to the older version instead until another MAME sneak in onto iTunes or Google Play.