And only two of them had any kind of presence. In any case, what you're suggesting is a serious step down from the previous films, where the villains were actual characters.
My biggest problem with a Sinister Six film is that there is nothing personal about it; there is no kind of personal journey in fighting six villains who, for the most part, have been rehashed from previous films.
Your points are valid... and I'm acknowledging that it would be VERY difficult to pull off.
But people seem to think that either ALL of the members of the Sinister Six have backstories and origins and personal connections to Peter, or NONE of them do.
Now, I'm not saying Sinister Six is the way to go, but if they did, they'd have to do certain things. First, they couldn't have the original lineup. If Kraven shows up in the movie with Lizard, he'll almost certainly die. He's out. Sandman and Doc Ock aren't really reasonable either, especially since, even if you COULD devise a plausible explanation for their return, showing that would eat up a good chunk of screen time. You can't just bring one of those guys back and expect him not to be the dramatic focus. So, of the original lineup, that leaves Electro, Vulture, and Mysterio.
Secondly, you'd have to set it up over the course of the movies before it. You couldn't just put the whole story together in one movie. The leader (let's say Hobgoblin) would have to be developed over the course of the trilogy, which could be done. At least one of them could be a featured villain in, say, Spider-man 5 (or 6, assuming that this would be Spider-Man 7, probably titled The Amazing Spider-Man, and not taking advantage of the whole "6" thing). The one that doesn't die, let's say. Let's say that Mysterio, coming back from a Scorpion/Mysterio Spider-Man 5, where Scorpion (who was the main dramatic focus) dies. Okay. Hobgoblin and Mysterio are set-up, and Mysterio won't need that much dramatic attention. He's not going to have any life-changing epiphanies, and, while he's not just a background character, doesn't need much more focus. Then, two of the guys can essentially be minions on par with Toad and Sabertooth. Let's say Rhino and Shocker (or Chameleon). They won't take much focus.
So, so far, we have Hobgoblin, Mysterio, Rhino, and Shocker (or Chameleon). That's four. By themselves, they won't eat up too much focus. The next two guys are, of course, Electro and Vulture. Vulture could be introduced as a character in the previous film, but become the Vulture here. He would receive about the same amount of attention as Mysterio. He'll be the most difficult one to balance.
And the last guy is Electro. The true star of the show. He's the dramatic focus, and the headliner. He's the one who can cause the most destruction, and the one who would undergo the most character development. And I won't repeat my whole spiel about how Electro could be done, because everyone who cares to read it probably has. But that's how he could be done. And essentially, what you end up having, is Hobgoblin and Electro as your star villains, Mysterio and Vulture as your second-tier, and Rhino and Shocker (or Chameleon) as your third-tier henchman guys with no real development.
And yes, I know, that's a B-rate Sinister Six. I'm not sure Sinister Six should be done, but I'm fairly certain it COULD be done, and if they did, they'd be the (or rather,
a) way to go.