I read the AMAZING SPIDER-MAN script during its filming -- and then I sadly lost the PDF in a computer failure, which is to say I failed to copy all my files to my new computer and sold off the old one. There's probably a netbook floating around this city that has the PDF on its hard drive.
My memory's a little fuzzy, but in the draft I read, Uncle Ben's murderer goes uncaught -- and that was the central arc of the film. Peter becomes Spider-Man for revenge, but he learns more about his father through Curt Connors, Peter realizes his dad buried his research to prevent it from being used to make weapons. To protect people.
Peter stops searching for Uncle Ben's killer, instead searching for people to help. The sketch of the killer, at the end, simply meant that Peter would keep an eye out for this man, but Spider-Man was no longer about settling the score. But Sony cut almost all of Peter's discoveries about his father. In doing so, they cut this arc.
On a side note -- I think the idea of a Spider-Man cinematic universe was really stupid and I follow Spider-Man religiously. Spider-Man has a great supporting cast and a terrific rogues gallery, but I can't imagine them being sufficient to lead their own films without Spidey in the main role.
In the comics, Spider-Man's world is populated by the Avengers (who regarded Spidey as an ineffectual child playing superhero until recent years), the Fantastic Four (who regard Spidey as a child except for the Human Torch, who considers Spidey an equal), the X-Men (who scare the hell out of Spider-Man with their dark futures and soap opera) and the Silver Surfer, Thor and Loki (whom Spider-Man would prefer to avoid because they're out of his league).
Restrict the Spider-Man Cinematic Universe to characters tied into the Spider-Man rights and you have mostly villains. Villains, by their nature, are not designed to be lead characters and Spidey only has one strong anti-hero antagonist (the Black Cat). SINISTER SIX and VENOM are film proposals where you'd be expected to cheer on the bad guys, an unlikely proposition for the superhero genre. The thing about most SPIDER-MAN comics is that the best tend to be comedies and his villains are meant to be a bit silly.
I don't think you can base an entire film on the Shocker and Hammerhead and the Gibbon and the Spot. And heroes from the Spider-Man rights -- I guess you've got the Rocket Racer, Frog Man, Puma and the Slingers? Most of these characters were designed as jokes to reflect some aspect of Spidey himself; they depend on Spidey as the lead.
Sony wanted a cinematic universe because everyone else seemed to be doing one; the fact that Spider-Man tends to be about Peter Parker was something they tried to ignore and I think it cost that regime their jobs. Not that the new regime is any better based on their new Sony Pictures chariman, Tom Rothman, and his track record of X-MEN: THE LAST STAND and X-MEN ORIGINS: WOLVERINE.
What should Sony have done? Personally, I would have used the cinematic universe elements that were suited to what was available -- which is cross-platform storytelling. I would have used AMAZING SPIDER-MAN as a big screen pilot for a streaming series.
The series would be computer animated using the pioneering cel-shaded format developed by the MTV series but using motion capture and voice acting from Andrew Garfield and Emma Stone. I would also have a series of video games that used the same visual style.
This way, SPIDER-MAN would continue as a series between films. I think with three or four 13 episode seasons, the characters would have come to mean even more -- and then Gwen's death in ASM2 would have meant something as opposed to being a discordant note. ASM2 could be designed to work for both people who've watched the series and people who didn't and be a big live action season finale to kick off another run of animated episodes. This format would be very focused on spending time with likable characters with movies and between movies.
Sony seemed obsessed with copying Marvel -- I think they should have, instead, drawn inspiration from Lucasfilm and CLONE WARS.