Why is the federal government responsible for airplane safety? Seriously; why is it a federal concern? Why does each airline, from small regional to transcontinental, have the same standards and practices?
Here's my thought: make safety the airlines' concern.
Sure, maybe there can be some slight minimum standards that apply to all, but in general let the air lines get their own equipment and make their own policy.
I think this would actually make a better experience for the customer, by balancing security procedures against market forces. If one airline let their standards dip too far, and their safety rating started to fall, they would have incentive to ratchet security back up. Of course, if they relax security protocols and, as I suspect would be the case, nothing happens, then travelers would have a less annoying, less invasive option. One airline could still be the "strip search and MRI for everyone!" airline, so those looking for a more "secure" experience would be satisfied.
It would give airlines something to compete on besides just price and who has the best peanut-alternative in-flight snack.
It would also provide benefits by allowing individual airlines to act as a lab, of sorts, to test new policies. I'm sure there are measures the federal government has not attempted because they are too expensive/impractical to roll out country wide. Smaller and more adaptable, individual airlines could innovate new security measures. The ones that work become part of the "minimum standards".