People pull Jerry Rice over and over and over as an example of how little combine speeds matter, but the reality is that a couple rare exceptions at the WR position (Boldin being the other) aren't great evidence that combine speeds don't tell us anything. For every Rice that plays faster than his timed speed, there's a dozen guys like Cordrelle Patterson, Marsquise Goodwin, Dante Stallworth that firmly establish their speed in the combine and other track workouts, and it translates on field. Of course, speed isn't all there is to a player, but saying that 40 times have "little to do with speed in pads" is silly. Occasionally, guys play at much different speeds than their workouts, but they're the exception, not the rule.
In the specific case of Wilson vs. Manziel, comparing their raw speed just seems dopey to me. They're both excellent athletes for the position that we can be reasonably confident will make plays with their legs. Neither is a transcendent athlete like a Kaep or Cunningham or Vick that's going to run away from defensive backs in the open field.
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People always say that, but if a team has enough internal information to be comfortable saying that a guy isn't going to be good, I don't really see the point in standing by a bad decision. The track record for guys that have rookie seasons like Geno isn't great. Maybe he'll wind up being good, but there's not really any reason at this point to even believe he can be a league average QB.