Why the drastic overhaul of the Spider-Man costume for the sequel? Gwen helped redesign it.
Somewhat confirmed in the tie-in Infinite comic - Gwen is the one who suggests Peter get a new costume, and they begin working on the new design after the original costume is destroyed in battle, with Gwen suggesting the bigger eyes.
When we see the dying Norman Osborn he is so sick that his skin is green and his fingernails are overlong; when Harry takes the spider venom, his skin turns green and his fingernails start to grow. Its entirely likely that Norman took the serum himself and suffered the consequences.
An interesting thing came up in the conversation between Norman and his son Harry. Harry mentions bitterly that Norman gave him scotch for his 16th birthday. Norman himself probably downed a ton of scotch throughout his life because it gave some form of solace from the fearful knowledge that an incurable genetic disease was slowing taking his life, so he figures that his own son may as well start "partaking" early since he's going to meet the same fate unless a cure is found.
I wondered why the location of Gwen's death was moved from the Bridge. Then it hit me. It was probably done to avoid being suspiciously similar to the climax of the first Sam Raimi Spider-Man movie which adapted this scene partly. Non-comic fans would probably believe the film was copying that film's climax and this franchise has already been subject to many claims of being a cheap copy of Raimi's films.
Not to mention that Spider-Man saved not only MJ but a whole busload of people in that version of the dropping scene. Changes were going to be made.
The clock tower also made a better setting for giving a reason why Peter had no other options besides using his web to catch Gwen and thus inadvertently killing her than the bridge would have been, better than the original scene in the comics even.
Catching Uncle Ben's killer was expected to be resolved in this movie, but the brilliance is it wouldn't have been good if it had. The reason is learning to let go of his petty vendetta and use his powers responsibly was a large part of Peter's character development in the first movie, and having him go back to searching for him would have been a case of Aesop Amnesia.
Peter's phone playing the Spider-Man theme might seem to be Leaning on the Fourth Wall, at first; but, considering what a huge fan base Spidey has In-Universe, it makes sense that somebody would have made the song as a tribute to him.
This movie basically does the exact opposite of the Rami trilogy. While in the old films, Peter and Mary Jane try to make their relationship work, but never can. In this film, Peter and Gwen keep trying to break up, for her safety, but they just can't stay apart. It comes off as a hell of a lot more adorable.
The clock hits 1:21 when Gwen hits the ground dead, Amazing Spider-man 121 is the issue Gwen died in the comics
Electro playing his own music during the final battle actually does serve a purpose: it demonstrates that he now has complete control over his powers, enough that he feels safe wasting them in some fun ways while toying with a spider.
When Peter talks to Harry as Spider-Man about not giving Harry his blood, he cites as a reason that their blood might not be compatible. It's entirely possible that they don't share the same blood type, which wouldn't help Harry if that's indeed the case.
After his incident with the electric eels, Max wakes up in a crematorium. That incident technically killed him. If he hadn't become electricity incarnate...
More squick than anything, but Max took clothes from the crematorium because his had turned to ash. Those clothes probably belonged to another body that had been cremated.
The Stacy boys have lost their father because of Spider-Man, and now Gwen has died because of him. Supervillains have been born from less.
If Electro is some kind of all-powerful electricity sponge, the consequences would have been far greater than a mere mundane blackout. He should have absorbed the electricity of people's nervous systems as well, killing everyone in the city. That would have been more realistic... and terrible.
The series has been cancelled to make way for the Marvel Cinematic Universe version. As this movie had a Bolivian Army Ending with Spider-Man in mid-battle with the Rhino, the audience can infer that Spidey died shortly after the credits began rolling.