I know I'm a dork, and it's a pretty good movie regardless, but I always hated the way they changed these important events in the Spider-Man mythos.

Spider-Man didn't effectively kill the burglar. He captured the burglar after Uncle Ben was killed when the burglar broke into his home, after which the burglar served time in prison, then died of a heart attack after release when he tried to break back into the Parker home where he had stashed a large sum of stolen money.

Also, Peter didn't even know Mary Jane this early, and they co-opted a very important (later) story line where the Green Goblin threw Peter's girlfriend off of a bridge. In that story line, the girlfriend, Gwen Stacy, died, possibly because of a broken neck as a result of Spider-Man trying to catch her with a webline.