I know we're talking about college football, but the dual threat conundrum has a lot to do with the NFL.
These athletically gifted QBs and Heisman Trophy winners are coming into the NFL and making their mark. Kind of. For a couple seasons. Then they get injured. Or defenses figure them out. Or OCs pressure them to pass first and run second. Or run only in an emergency. And some of them lose their edge and mojo, like Vince Young or RGIII. And then you look up and realize it's still a game ruled by classic drop back passers. Maybe Russell Wilson and Colin Kaepernick aren't the future.
Marcus Mariota may do just fine in the NFL, but as extremely talented as he is, the number one concern at the combine was whether he could run a pro-set offense.
Top college football players, the handful with NFL potential, raise their stock signifcantly by working in offenses familiar to the NFL. I can see the zone read living on like the old triple option before it, or a WR reverse, or a fullback counter. A play you pull out every game or two, but not your offensive system.