Eggman has been the central villain in every game aside from ShTH, Finalark. He just gets upstaged at the last minute by an even greater threat.
The plot of Sonic Adventure pre-Super Sonic's story revolves around Sonic and co. trying to stop Eggman from destroying Station Square with his Egg Carrier and Chaos so he can build Eggmanland in its place.
Sonic Adventure 2, he's presented as the villain all the way until the self-destruct program that Gerald installed activates. Shadow wasn't even aware of this secret program, only knowing that the Eclipse Cannon can be used as a legitimate threat and as a leverage of power for Eggman.
Sonic Heroes, everyone is led to believe he's the main villain until skepticism arrives when Metal Sonic reveals himself at the end of the Egg Albatross fight.
Sonic 06, he's one of the major villains alongside Mephiles and Iblis, and the star villain in Sonic's story.
Sonic Unleashed, Eggman successfully proves that he can defeat Super Sonic, just as he did with his Big Arm machine years ago, manages to awaken Gaia, and as Sonic is wondering the earth trying to resuscitate the Chaos Emeralds, Eggman manages to harness Dark Gaia's power using his machinery so he can use them as a main force, and finally accomplishes his goal of founding Eggmanland.
Point is, an argument can be made that Eggman WAS the real villain, or at least the central one, in these games. He's just not the final one in most of them, as he gets upstaged by a more looming threat.