As a matter of fact, I'm convinced that instead of Sandman and Venom, the perfect villainous duo for the 3rd film would have been Shocker and Scorpion. Think about it: With both these guys, you once again have two villains with the kind of weaponry and enhancements that aren't that far off as the Goblin or Doc Ock so the feel of the movies still feels consistent. With Shocker you have a guy who can blast Spidey from a distance and wear a suit that can absorb his punches, making him a threat at any range. With Scorpion, you have a guy who can match Spidey in strength, speed, and agility like Venom could but you also have that whip-like tail to bash Spidey around like Dock Ock's tentacles did in the second film.
You can still have Harry attack Peter like he originally did, but instead of getting amnesia, he'll lose badly to Peter and just become so determined to take him down that he’ll try to develop a special suit to help gain an edge (ie the Scorpion suit), which he can hire Mac Gargan to test out. You can still have that whole story of Peter finding Uncle Ben's killer, revealed to be a wanted burglar, Herman Shultz (which I think would easier to buy than the Sandman we were obviously supposed to sympathize with) who has resurfaced and somehow obtained his new suit and power gauntlets, becoming Shocker. Gargan can test out his Scorpion suit by fighting Spider-Man, and maybe even nearly beating him, but then go insane once he sees what kind of freak he's become and then start to set his sights to get back at both Harry and Spider-Man.
You can also still have the subplot with Peter wanting to propose to MJ, but instead of making them both so damn whiney about it, the conflict Peter faces is whether or not he can really risk bringing MJ into his dangerous lifestyle, especially after dealing with the Scorpion hunting him down.
Of course, Shocker and Scorpion can eventually team up to take down Spider-Man , with Harry joining to help him after he comes to revelation as how Peter was always his friend or some other such BS.
And MJ (instead of being the damsel in distress for the 3rd ****ing time in a row) can of course do something as well to help them, like maybe distract Scorpion so Spidey can get the drop on him, thus showing she’s perfectly capable of handling Peter’s lifestyle. In the battle, Scorpion will die in the fight, but in his last moments he’ll still try to sting Peter with his tail, which Harry will take instead, redeeming himself, but also putting him in a coma. Shocker will be stripped of suit and arrested and of course you can have that clichéd moment where Peter looks like he’s about to finish Shocker off and avenge his uncle but stops himself from doing it.
And blammo, there's your movie.