He flew under the radar because he was seen as a developmental prospect who put up monster statistics against inferior competition.
Kaepernick would be a top 10 pick if that draft was re-done. He put up huge numbers against just about everybody (PAC-10/12, ACC, WAC, MWC, BIG 12).
The offense that he played in scared teams away. He didn't take snaps under center/didn't drop and he usually read half the field.
He was seen as a developmental prospect. That's fair to him. Marcus Mariota should be seen the same way.
I do not want to use a top five pick on that kind of player.