I'm a stats guy. I'm aware Elway was thought of as a good runner, but he had negative rushing yardage every year in college (sacks). Guys like Drew Brees even had a 500-yard rushing season - they took that skill and made it a positive that could be measured.
Just as Raghib Ismail may not belong at #25, I definitely have a halo effect for him EVEN WHILE KNOWING HE ONLY SCORED 15 CAREER TDs, I just feel you have a similar effect with Elway. I don't doubt for a minute that the consensus at the time was that he was an all-world great player, both ability and production-wise.
But Wuerffel has better Heisman/awards data AND better passing data (both rate and percentage). For me, that's it - case closed.
Along the same lines, I don't think Randy Moss should stay on the list. He had 2 huge years at a G5-type school. He was good enough to play at ND or FSU, but he screwed up and ended up at Marshall. So his highlights are vs Army and Ball State instead of Michigan and Miami. His NFL HOF exploits shall not be taken into account, and his college production takes a hit due to the schedule he faced.