Honestly, if you wanted to make the Spiderman films better in my eyes you would need to do a couple of simple things. It doesn't involve the villains or the story. First off is the biggest issue. Toby Maguire is just not right for the role. I don't have a huge problem with him, he's just not Peter Parker. Peter Parker is extremely smarmy. The more smarmy banter that Spidey has, the better. Its one of the reasons why he's such a great character. In addition, the Spiderman, they portray isn't Spidey. Spidey is the sort of gangly, loose hero who's movements actually look kind of spider-like when he swings. Spiderman in the films is built, no gangle. It just... doesn't look right. In the same way Kirsten Dunst is just... not Mary-Jane.
Then I guess you have to pick the right villains. Interesting ones. Kraven is pretty cool. Vulture had some good stuff going. I was always a big fan of Kingpin and Smythe, but I guess that was more the 90s cartoon than the comics I'm basing it off of.
On a basic level, the movies just need better casting. The people they pick just aren't right for the roles.