What about Life Lock(?) mode, or is that a "Perfected" Omnimatrix feature? Besides that and Master Control, there aren't many deliberate features for Taylor to mess with.
Hmm... How would the Genetic Repair function work? Like, could it cure genetic defects, or are we talking exclusively severe genetic damage? Oh, and there's how Ben saved the Highbreed by turning them into hybrids.
Then there's the possibility of Taylor discovering the Gene Scanner function, as well as accidentally achieving hybrid forms. Wait a minute, I just realized... Could we turn into Upgrade and promptly target the Omnitrix?
Reboot!Ben did exactly that for his Season 1 finale, unlocking Master Control temporarily that way.