The NBC Olympic website has posted some useful material for making an informed judgment on this issue; under Expert Analysis, they have "Scoring Analysis" for both Lysacek's and Plushenko's free skate, where they show the scores for each individual element of the program. Based on that, as well as some of the other expert commentary, I would say that Plushenko's biggest weaknesses, the ones that worked against him the most, were (1) sloppy landings on two big jumps, (2) not enough complexity in his footwork sequences, and (3) putting his more difficult elements in the first half of the program; under the new system, they get a bonus during the free skate for the elements they do after the halfway mark, so most of the competitors save their more difficult elements for the end so they can take advantage of the bonus and really rack up the points.
For better or worse, famous athletes are role models. Plushenko vocally complained about the competition and next thing you know his countrymen are following his example by crying foul. Now, there is something to be said for loyalty, and even Evan Lysacek commended the Russians for supporting Plushenko. On the other hand, I think there's a time to stand behind your defending champion, and a time to stand up for what is right. If the tables had been turned and it was an American whining that he'd been robbed when he was beat fair and square, I would not support that kind of behavior; I'd be embarrassed by it. By the same token, if Plushenko had had a legitimate complaint about the fairness of the marks, I would absolutely support him, because I don't believe that national allegiance should take precedence over fair play.
That being said, I just can't praise Evan Lysacek enough for his performance on the ice and his behavior off of it. He has represented our country so well by his athleticism, of course, but moreso by his positive attitude and good sportsmanship, and therefore serves as such a positive role model for us. As a nation we have a reputation, not entirely undeserved, for being arrogant, and so it's so refreshing to see an athlete take the high road like this. While Plushenko is taking verbal swings at him, Lysacek is turning the other cheek, but at the same time he has taken complete ownership of his accomplishment, never once deprecating himself or downplaying his performance, which goes to show that there's a difference between being humble and humiliating oneself.
I've been trying to access the Canadian coverage of the event from CTV. Their commentators were Jamie Salé and David Pelletier, the pairs skating team whose silver medals were upgraded to gold after the judging scandal in 2002. It would be really interesting to hear their take on it, since they know first hand what it is to be robbed of a medal. But at the moment, the CTV website seems to be having technical difficulties.