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1. Keith Price's decision making has improved a lot over what is was a year ago, but it's almost as if it has improved too much. Oregon has one of the best secondaries in the country, but I really doubt that there was so frequently nobody open to throw the ball to. When that happens, he's go to either throw somebody open, or just let a guy like Kasen Williams make a play on a 50/50 ball. At some point he needs to be a playmaker and make a play, because he's not always going to be able to rely on having a perfect throw to make every time he drops back.
2. The Husky safeties are atrocious in pass coverage. This was the first game this year where they were really forced to consistently be in coverage and they were exposed. Sean Parker and Will Shamburger consistently let Ducks get behind them and didn't have the speed to track down players who had caught the ball in the open field. Whatever problems the team may have seemed to have coming into the game, this is the biggest concern heading into the second half of the schedule.
3. Austin Seferian-Jenkins is still a potent weapon, though I'm not sure the way the offense is run maximizes how well he can be used. The way the offense is currently run involves a lot of unbalanced formations in which the tight end is covered up by a wide receiver and is rendered ineligible as a pass catcher. It can create an extra gap in the running game, but I'm not sure that the best way to utilize your All-American tight end is to have him as basically a 6th lineman on a good chunk of plays.
4. Moving away from the short passing game has been a mistake. In the early games of the season the behind the line of scrimmage passes were easy money, giving the offense chunks of yards at a time at very little risk or effort. Oregon and Stanford's perimeter players are good enough to break them up more often than teams in the past, yes, but if they do then it's no worse than a stuffed run. However, the likelihood of Jaydon Mickens making even the Duck defenders miss is pretty good, and that turns into a pretty big play quickly. It would have been at the very least worth a try to attempt to get the passing game into a better rhythm.
5. Oregon is really really good. Marcus Mariota is a transcendent player, who probably already has the Heisman sewn up. To shut their offense down, you've got to be able to make Mariota uncomfortable without blitzing, have linebackers with speed enough to chase him down if he scrambles, and you need a bevy of defensive backs who can play their receivers straight up. There aren't any defenses like that in the Pac-12 this year, and generally aren't more than one or two in a given season.