I think it goes beyond that; I think it becomes incumbent upon the GM to play those Limitations. That doesn't mean that if the character has (say) an OIF it should be taken from him 33% of the time, just that there is some likelihood of that Focus being taken away during combat, malfunctioning, being immediately unavailable, or even stolen. It doesn't have to be the whole scenario, just during it.
As an example: a powered armor type in our campaign was once kidnapped while in his Secret ID after his helicopter was shot down; and was unable to put on the suit he was carrying in his briefcase because his kidnappers just left the briefcase in the wreckage. He ended up having to escape from the bad guys without his armor; which ultimately let the player experience one of his favorite adventures. So in that session he got hit with both one of his Limitations (OIF) and two of his Disadvantages (Secret ID and Hunted). Of course, the key to his escape was another DisAd, because the character's DNPC girlfriend was an expert SCUBA diver and it was only logical that our hero would have gone SCUBA diving with his girlfriend even if he lacked the TF. So he managed to swim to safety (he was being held on a yacht at sea), recover his armor, and fly back to stomp the badguys.
That's one of the advantages of building characters as opposed to stacks of numbers. The player was so enthused by the experience he ended up buying TF: SCUBA.
"I think it goes beyond that; I think it becomes incumbent upon the GM to play those Limitations."
Ok so if that's the style of play and GMing it was priced for and I don't care for running it like that, I guess the value of the limitation should probably be less.