The movie is extremely cluttered, rather like Iron Man 2
in its attempts to serve various different corporate purposes, though it's better than Iron Man 2
because the central emotional arc of Peter and Gwen is well-done, and the film has a strong finale.
The plot and the villains, on the other hand, are extremely scattershot. Electro is basically Jim Carrey's Riddler (as noted by Drew McWeeny at Hitfix), by way of Doctor Manhattan. Harry's whole story feels rather rushed (particularly as he acts like he's going to drop dead at any moment when his father lived to be like three times his current age), and the structure of the climax, with him arriving after Electro, feels tacked on. That said, Gwen's death and its aftermath is well-done.
The single-biggest problem is the Richard Parker backstory. Why did anybody think this was a mystery worth dragging out over two films? The "revelation", such as it was, is totally meaningless to the story apart from a I guess a bit of trivia about why the spider-venom only works on Peter, but that really didn't need a whole subplot to explain it. The whole thing could be excised without impacting anything else in the movie. Though I'm glad they at least avoided the idea that Peter was "destined to be Spider-Man" or whatever.
Also, the ending hints at how future Spider-Man villains will be handled: as mooks for OsCorp. It's far from unheard of for OsCorp (or a similar company) to be used as a linking point -- it was in the Spectacular Spider-Man
cartoon, for instance -- and for some villains (like Rhino, in this film, or Shocker) that sort of origin works. But the end of this film suggests that Doctor Octopus and the Vulture are also going to be created this way, which is a terrible idea, as those characters actually have somewhat meaningful origins of their own (especially Otto).