There are several categories they scout on:
Athleticism
This is important because NFL defenses are fast, they are going to rush you faster than college defenses, the Safeties and Corners are going to be faster on blitzes, and plays are simply going to happen a lot faster. This is where a guy like Johnny Manziel succeeds. He has a lot of Athleticism, he can make plays with his feet, get out of the pocket, etc.
This also has to do with height, weight and speed as well. A tall, big armed QB is prototypical for an NFL offense, that's why guys like Ben Roethlisberger succeed, but then again, you have guys like JaMarcus Russell who don't, so that can also be a hit and miss factor.
Arm Talent
This is just as it sounds, how far and accurate is a Quarterbacks arm? Can he throw it far, can he throw it accurately, can he hit the small windows that will be in a lot of NFL games. As in the Super Bowl, can the QB make that game ending throw, on target, for the Seahawks to win the game instead of throwing it into the defenses hands, a little behind the WR instead of in front, and the game looks different. Obviously that doesn't mean Wilson can't make the tough throws, but you get the gist.
Pocket Presence
How does a QB play in the pocket, with NFL defenses rushing down your throat, how do you react. Do you get caught off guard a lot? Do you panic when you're getting rushed? Do you make bad passes when you're feeling the pressure? Anything to how you do while you're in the pocket, and waiting for the play to develop. This is very important as it shows your composure in the pocket when you have 2 or 3 350 pound lineman looking to crush you.
Football Intelligence
This goes a long way in recruiting, and as you stated, Russell Wilson has a lot of it. How will they do running a complex offense? How will they do reading different types of defenses to know who they should throw it to, and who is lurking around what WR? A quarterback is asked to do quite a bit in the offense obviously, so he is going to have to be the leader, the guy who knows it all, the guy who can read the defense and tell what passes to make.
Clutch Factor
This is something that might or might not be high on peoples list, but again, goes along with Russell Wilson in the Super Bowl. Although he threw a bad pass, he worked the ball down the field pretty quickly and efficiently(helped a lot by that great catch, but still). Things like that will make a QB more appealing to a scout. How likely is it that he can stay composed to lead you on a 4th Quarter Comeback? How does he play under pressure of being down late in the game? Can he still make those accurate passes? Etc.
Character
This can either be high on a list, or low on a list, do you want a QB that will follow all the rules, be a good person, and win you games? Or do you not mind if they make a few mistakes, party every once in awhile, and still win you games, but has the potential to get in trouble from time to time. This has a lot to do with the coach as well, in a sense of, "Can my coach handle this type of player, and keep him in line?", etc.
This and many other things are what scouts look for in a QB. But you also have to understand, even if a QB has all the right tools, doesn't mean he'll succeed. These things can only go so far in telling what type of QB he'll be. So yeah, teams are going to miss on QB's from time to time, and sometimes they always miss. Take Ryan Leaf for example, huge QB prospect, had all the things you want in a QB, but just couldn't make it work in the NFL. It happens.
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