Route running most definitely matters in the NFL and it matters more than anything else. That doesn't mean because a guy isn't great at it in college that they can't or won't learn it, but it's one more box to check on their way so the learning curve is longer. It's not just learning what the routes are, it's learning how to run them crisply and sell them against the defender. Also, athletic abilities don't mean a guy will just become a good route runner. They need to have the dedication and drive, as with any other player doing any other thing, to get better at it. Not all of them do though, and I'd wager a great many. It wouldn't preclude me from taking a guy, but if two guys are sitting there with fairly identical traits, I'm going to take the better route runner 10 out of 10 times.
That said, there are rarely two identical physical prospects out there but one runs shit routes and the other doesn't. And generally, there are other factors at play too aside from just routes. Athleticism and the ability to catch in traffic are definite factors. All 3 factors came into play last year when I looked at Elijah Moore vs Rondale Moore who were similarly-sized prospects with similar NFL positional outlooks.
Given the overall complexity, you have to slot guys based on the potential of all things. A guy can learn to run more sophisticated and more crisp routes. A guy can develop better hands. Guys can't learn size, speed (limited), or physicality. There's a reason to take Pickens over say, Skyy Moore or Jahan Dotson. While Moore and Dotson have high floors and could be 1k/6TD WRs, they simply lack size, athleticism, and the physical ability to just beat anyone. Pickens has those things, and if he learns to run routes well and stays healthy he will beat anyone and could be a 1500-yds, 15 TD WR that forces the double-team and makes defenses adjust to them.
Pickens is oozing with elite potential and he's not "that" far away from reaching it. A guy like Watson though, he's much, much further away than Pickens. Now you have to start wondering if the investment into getting him there will be worth the return (before he hits FA and is doing it for someone else), if it ever is. That's where I think you take the higher floor guy, when the high ceiling guys start looking like too significant a project to make sense at that draft position.
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