It's nice to see a different take on Spider-Man 3, even if I don't entirely agree with it. However, on most points I am totally with you. Peter Parker, or at least this incarnation of him, is a massive dork. It made perfect sense that he would be trying way too hard to be cool and I liked everything right up to the Jazz sequence.
For me there are three unforgivable flaws this film committed which allow it to earn it's reviled status.
1. The Mary Jane dumps Peter to save him. This was tired cliche by the time this occurred and it is handled so poorly. Peter weeping like a crushed child doesn't help either. Seriously, Peter is Spider-Man, why doesn't she just tell him, "Hey, our mutually crazy friend is trying mess with us, go punch him the face." or "Hey, I don't really mean it, Harry is just making me say this, sorry to make you weep like an 6 year old with a skinned knee."
2. Uncle Ben was really killed by Sandman, but it was totally an accident. This IS as bad as Batman's secret Joker origin. Worse even, because the original scene was perfectly handled, and this goes back and retroactively ruins it. Even worse yet, this is completely unnecessary. Just have the Sandman show up at a robbery and hurt one of Peter's friends. Boom: motivation.
3.The entire 3rd act. Seriously, it's terrible. The film by this point just goes by the motions, ticking off everything that happened in Spider-Man2, just done worse. Mary Jane get's kidnapped. Goblin Jr. learns he has the world's worst butler, that his dad was really the jerk, and he get's a last minute change of heart. However, the worst part about is, that the film resolves nothing about the Peter and Mary Jane relationship.
Like I said before, I appreciate a defense of this film, especially with all the dull-witted attacks that get dumped on it. Not everyone who dislikes this film is an idiot, but a majority of them really can't be bothered to say anything more than make a gay or emo Peter joke. However, despite it being a disappointment I will take watching this over Amazing Spiderman any day of the week. S3 is failure that could of been prevented had Raimi insisted on a rewrite and was able to fend off studio interference. Amazing Spiderman is a cynical cash grab made just to keep the license going.