If the villains were as awful as you say, then i think that the film would get more negative reviews, especially from the fans. If you visit the poll thread you will see that most people gave the film an 8 or a 9. That means that the villains also worked. From what i gathered the villains didn't overstuff the plot. The parents's storyline did.
If you look at the rating thread for Spider-Man 3 here from back in the day, it had 1190 ratings, and over 868 of them gave it a 7 or higher:
http://forums.superherohype.com/showthread.php?t=270765
The shine will soon wear off for some of those who vote it highly I think, just like it did for the high SM-3 votes.
No one is reinforcing anything besides personal opinions.
And the popular opinion is the movie was too crowded. That is the general consensus. So to suggest Webb succeeded with the multiple villains is a fallacy since most people were not satisfied.
I think Webb showed how you DO Handle multiple villains. 1 has to be very minor, while the others need a connection that makes sense. It can't be a random "hi how are you, kill kill kill" like spidey 3 was...
That's a fallacy, too. Harry wanted to kill him for revenge for his father. Sandman wanted to kill him because he tried to kill him first. Venom wanted to kill him because he had him humiliated and fired. It was not just random kill kill kill. All the villains were established with solid motivations, in Harry's case he's been developed since the first movie. Something no villain in TASM 2 can claim.
But all three of them were rush jobs. Oh look here's Harry, he's best friends with Peter, he needs his blood but Spidey says no, KILL HIM!!!. Oh look here's Max Dillon, he met Spidey for 20 seconds but he loves him now, oh wait Spidey forgot his name...KILL HIM!!!! Look there's Aleksi the Russian mercenary, Spidey caught him in the middle of heist, give him a Rhino suit and KILL SPIDEY!!!
That is the guidebook on how to not do multiple villains. It was all a rush job to set up the Sinister Six.