That's an easy fix; more TSA and more runways.
The cost of putting in a few new security checkpoints and a couple of extra runways is nothing when compared to what a hyperloop will cost.
If LAX had 8 runways and a terminal structure that made sense, it'd never have delays. If SFO had even an extra 2 runways that weren't three feet apart, they'd be able to run parallel ILS approaches and boom, no more delays, and no more, "I know you're IMC, and I know you can't see the traffic...or the airport, but you're cleared for the visual anyway" from NorCal.