Does Kingpin still count as a central Spidey-villain? He's pretty much the Luthor in Spidey's universe, though I don't really count Luthor as a main Bat villain. And Norman Osborn can easily replace him.
Teamwork aside, I think Bat's side edges out slightly just because they, like I said before, are more "mature" and cunning. But then again, most of them don't want to work together since they got their own diabolical plans. It even amazed Batman how the Riddler could gather up all the Bat villains to mess with him in the Hush series, and Ra's Al Ghul didn't want any part in it.
As for Spidey's teams, they have formed A LOT and MANY MORE TIMES. The different versions of the Insidious Six. GG is also good at organizing. However, they do botch up a lot since like I mentioned before, they seem to be more "immature" than Bat's villains on their quest for world domination and end up messing each other up. Yet, if they know they have to take down Bat's side, I don't even think they need that much teamwork. All their powers combined is just too massive.
Joker runs in with his gun and acid, BAM, Shocker blows him to pieces.
Clayface charges....Rhino charges back, Hydroman douses him, and Sandman smacks him dead on...Electro can give him a massive lightning shock. Too many possibilities. And I can't think of anyone else that is up to the same strength caliber....Charaxes? Even Croc is just slightly superhuman, but NOWHERE near Lizard, Scorpion, Rhino or Molten Man. Grundy, perhaps, but still....for every one super strong Bat villain, there are 10 more Spidey villains (Class 10 ton, 20 ton, 80 ton range) to take his place. For every psychotic Joker and Zsasz, Spider-man can find Carnage, GG who are ALSO super-powered.
I'm not sure Ivy's charms can work on superpowered villains, but I guess if they can work on Superman, it's possible. She might be easily dead before she even gets close though.
With Prep time, maybe Bat's villains can coordinate something...but as it is with most of these fights, they are a result of a random gathering.
Bat Villains:
Joker & Harley, Two-FAce, Ivy, Penguin, Riddler, Ra's, Ventriloquist, Croc, Mr. Freeze. Bane, Catwoman (yes, I'll list her too), Scarecrow, Hugo Strange, Man-Bat, Shiva, Deadshot, Clayface (all versions), Mad Hatter, Cornelius Stirk, Firefly, KG Beast, Abbatoir, Ratcatcher, Killer Moth, Zsasz...
Spidey Villains:
GG (all versions), Scorpion, Hobgoblin (all versions), Lizard, Doc Ock, Kaine, Morlun, Carnage, Venom, Shocker, Shriek, Tarantula, Sandman, Hydro-man, Molten Man, Vulture, Mysterio, Chameleon, Carrion, Morbius, KingPin, Rhino, Tombstone, Beetle, Jackal, Kraven, Manwolf, Puma, Hammerhead, Rose...
...and I'm not even mentioning the League of Losers...and characters like Boomerang, Walrus, or Tinkerer.