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To be honest, I went in expecting much worse than I got when I watched the replay. I don't think we were lucky to win that game at all--I think we were the better team. SJSU can point to some bad calls, without question, but on the other hand their DBs really were generally mauling wideouts; maybe the exact calls weren't right, but the distribution seemed about right to me. Stanford could've had a couple picks that just missed, and could've had a couple of TD passes that just missed. I thought the game was pretty neutral, luck-wise.
Overall, I think the game was concerning in the short-term but medium- and long-term doesn't affect my outlook too much. The main problem was the offensive line's run-blocking; as we've discussed elsewhere, we've had slow starts from an OL perspective in 2009 and 2011. With the amount of talent we've recruited at the position, there's really no reason to expect anything other than--at least--a very good offensive line. Whether it gets to the level to enable the rest of the team to work is another question. I felt the pass protection was pretty good in general, so I think it will be by the end of the season. It'll look unsightly at times, but I think we all expected that. Nevertheless, missing out on three 3rd/4ths and ones is really unacceptable.
Nunes was basically fine; the question is, is that an omen for expanding what he does or did he only play fine because his role was limited? It looks like Nunes has the arm to make all the passes, though not spectacularly, and his decisionmaking was generally sound. I would like to see him be more accurate in placing the ball--a few of his completions should've had better YAC if the ball were placed better--and have fewer balls batted down by the defensive line. He looked crisp and competent running the two minute drill, and didn't panic when things looked dicey at the end of the game. That's a trap a lot of favorites get into when the underdog starts to challenge them--panicking, trying to do too much, etc. Nunes didn't fall into that. He'll be a competent quarterback for a year or maybe two, depending on the development of Nottingham, Hogan, Lloyd, maybe Burns.
The question is how much they give him to execute. Obviously I agree with most people that more downfield plays should've been called, but I'll add in another criticism: the coaches should also explore stretching the field horizontally. This was the approach used in the first two drives and it worked pretty well.
In fact, the weirdness of the game starts with the first two drives. Basically the team executed tolerably in the first two drives and had a decent chunk of the playbook available and scored each time. I'm not sure why the coaches backed away from that approach, but it's what allowed them to even it up. The coaches, it seems to me, got overconfident. Shaw is accurate but not wholly truthful when he says execution was the problem on offense. If the run blocking were better, the team would've won quite handily; nevertheless, the coaches could've done better with playcalling. (Also, a subject re: run blocking: Lee Ward didn't have a good game, I think, and missed a couple of critical blocks; also seemed to be a bit slow for the Spider 3 Y Banana. Hewitt will be a nice upgrade there.)
Defensively, again, it was a weird instance of the team changing its approach after a couple of drives. In this case, in the first quarter or so, the corners played tight; thereafter, they played off, loosely. I'm not sure why the defensive guys went away from a successful approach, but one hopes the mistake isn't repeated. THe defense had three adequate/good quarters and one poor one. While below our expectations--and Shaw's, judging by the postgame press conference--I wouldn't at all call it the weaklink. That was the offense.
The special teams were solid. After Brian Polian's reign of error, it really is a comfort to have a special teams submit a performance in which nothing goes wrong. If Alamar can deliver this level of performance throughout the season, the special teams will be significantly improved from last year.
If Shaw and staff are average, collectively, the team will be much better by the end of the season than the beginning. The question is, for me: a) how quickly does the improvement come, and how high is the level of improvement and b) while the team is still learning, how many wins can the team engineer in less-than-aesthetic ways? That's what I'll be watching.
EDIT: one more note. It seems like the emphasis the coaches put on getting more turnovers, particularly INTs, was in effect on Friday. It looked like the defense tried to jump a few too many routes yesterday. Ed Reynolds, for example, was 1 for 2 in such route-jumping.
EDIT2: not also that cute/creative playcalling did not totally expire after the first quarter. Stanford had a very cute use of an unbalanced line to get Stepfan Taylor to the 1 yard line in first-and-goal. Sadly we weren't able to punch it in.