If The Omnitrix is truly a prison, here are the abilities that should come with it:
A. The ability to generate an Alien life form out of the Omnitrix and "Slave drive" it to do what you command.
B. The ability to "Radar" chosen alien species by tracking their DNA. Crime device for tracking down aliens.
The ability to create Mutant forms with the user, Osmosian or not. This would be a punishment, using their DNA with another being whether they like it or not.
Sorry for the short post!