Sonic 3 and Knuckles/WMG

Sonic & Knuckles is an unauthorized sequel.

 * Alledgedly, Sonic 3 was concieved as a standalone game, but far up north, two midgets somehow programmed a flawless imitation of Sonic's game engine and used it to create Sonic & Knuckles. They tried to pitch it to their boss, who thought it would never catch on. Fortunately, these two guys successfully sold the idea to Sega, and got rich off of it, despite Sonic Team taking credit for the game. A rare mini-documentary talking about it can be found here.

Amy could have been playable in these titles
She was meant to be playable in Sonic CD

Sonic's modern look and powers are side effects of turning Hyper Sonic.
As Hyper Sonic, his eyes turned green, just like his modern look. Sonic 4, taking place after this, is the first canon appearance of the modern look and the homing attack. The biggest evidence is that as Hyper Sonic, he could unleash a double jump attack the propelled him further and destroyed any minor enemies on screen, and with the general ability to direct his momentum, and now the boosting he's clearly growing in power.
 * As an add-on, exposure to Chaos energy is probably what turned his eyes green. The height could be explained by puberty.