What makes Kaepernick viable is that he's built almost like a skinny TE: 6'5" 230. For comparison's sake Tennessee TE Mychal Rivera is 6'5" 236. Fajardo is 6'2" 205. He's underweight even by mobile QB standards, and unless he's got that Barry Sanders' gene that Russell Wilson has as deflecting hits, he won't last as a running QB in the NFL. He's skinnier than guys like Michael Vick and RG3 who are infamous injury magnets. Most mobile QBs are built like thoroughbreds, but Kaepernick is built more like a workhorse. That might be the most valuable thing of all about Kaepernick. Fajardo probably isn't going to get the same usage in the NFL.
Fajardo has inconsistent throwing mechanics, on some plays he looks great, on others he's almost Tebow-esque. Kaepernick's throwing motion wasn't perfect, but his 95 MPH fastball arm compensated for it. Fajardo isn't a bad thrower, but he is a different thrower than Kaepernick.
I am shocked the Fajardo finished with the rushing yards he had. Maybe he's deceptive fast, but he looked really average to me as a runner. I would guess 4.7 or 4.8 range in the forty.
To be clear, I'm not ripping Fajardo. In some ways I think he could easily be a better NFL QB than Kaepernick is. I just think he'd be more of an Aaron Rodgers type than a Kaepernick type. He'll have to rely on his technique and intelligence as opposed to Kaepernick who succeeds based on pure physical ability and a scheme that makes life easy for him. In that sense, I could see the Seahawks being all over Fajardo as a mid-late round pick in a couple years.