To be honest, the story itself in the game isn't too bad actually. But it's very complicated to try and compare two different mediums. Though I'll do it anyway:
THE STORY
The story itself in the game is actually a very good follow up on the film IMO. This is where Beenox did a great job. It felt like a great story connected to the film without having to be brought up in any film sequel.
Of course, the film story was much, much more personal due to seeing the origin of Peter Parker/Spider-Man and his love story with Gwen, but also due to it having real actors. This is where games overall lack compared to films if you ask me, it's harder to feel connected the same way (with some few exceptions such as the Uncharted games which hit every note right).
However, the plot itself in the game is more clear than the one in the film. It goes more straight from A to B. This is obviously because the game doesn't have to deal with the origin and it has more time than a film, but still.
THE CHARACTERS
It hurts to say but I definitely think Alistair Smythe in the game was a better villain than Lizard in the movie. It's funny. I felt he had more depth and much clearer motives and overall was more interesting. Beenox did one hell of a good job here! However, I couldn't like Connors much in the game either. Peter and Gwen were great in the game but as I said, it's hard to compare to the film since they're played by real actors there and therefore I feel much more connection to them. But in the game, they both were written very well and Spidey felt more grown up in the game from what I remember. Though, the film had a great character in Capt. Stacy that the game misses and that Asian reporter wasn't that interesting to me.
OVERALL
I would much rather sit through the film several times again than the game but that's obvious. A game takes much more time and requires you to be more active. Though even with that fact put aside, I definitely enjoy the film more. But that's not to say that the game did a few things better (the villain and his plot, that is).
Though there are instances where I'd much rather play through the story of a game than a movie. As I said, the Uncharted games are perfect IMO and I many times find those characters, pacing, story etc. better and more enjoyable than some films. if Naughty Dog were developing a Spider-Man game, I don't doubt I would enjoy those more than many films as well. But that's a very rare thing.