I find this whole premise of "villain easily steals Starfleet ship or craft" quite implausible. That is, I don't think there's anything implausible about the thefts - the very existence of such a premise is what I doubt.
Who steals Starfleet craft? Ballparking the statistics, seven times out of ten it's authorized Starfleet personnel. They are entitled to using the hardware; there's no reason Security or Maintenance should suspect a priori that their takeoff is contrary to the wishes of the skipper. And there's no reason to lock the vehicles behind passwords unknown to Starfleet personnel - who's gonna fly the craft then?
Three times out of ten, the theft is by creatures who can alter the course of a starship by giving it a stern look. "Easily" is not a valid accusation there!
"Power Play" is a nasty combination of the two, and Security nevertheless stalemates the "authorized supervillains"...
Today's militaries might reasonably proceed from the assumption that their personnel hail from the lowest gutters of wrongdoers, and shouldn't be given keys to the tank unless guarded by an armed officer. Starfleet supposedly trusts all its employees, though.
Timo Saloniemi