They also have the biggest impact on the game, touching the ball every play. The rhythm of hiking the ball, hand offs to RB, WR relationships, are all things that aren't direct carry overs, and just trotting out a new qb every drive could have a bigger impact than expected (especially for an offense that can barely execute as it is).
It's also funny because plenty of teams DO switch Qb's when the coach thinks both can perform. We trotted out JT and Vad. We trotted out Marshall and Tobias. Last year Clemson was playing Uiagalelei and Klubnik.
Maybe Faulkner doesn't believe in using two qbs or maybe he and Key think QB #2 is not playing well enough to be a suitable replacement to #1.