Allegedly, 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.
- As an add-on, exposure to Chaos energy is probably what turned his eyes green. The height could be explained by puberty.
- This also explains Eggman's growth spurt between this game and Sonic 4, despite being an adult. In Doomsday Zone, you ram his final robot to destroy it and win the game. Eggman somehow absorbed some of Sonic's energy from the hits, causing him to grow.
So if he really wants Sonic dead, why not just set up a boss room that floods with poisonous chemicals, with no way out? Or trap him in a room for 10 minutes? Or have him fall into a boss room with an all spiky floor, that he can't jump out of, sort of like a certain pit in the Mystic Cave zone? Gameplay and story segregation aside, I think it's because Robotnik/Eggman knows that if he wins, things will get very boring very fast. A man with an I.Q. of 300 is likely a man who gets bored easily, and so when Sonic came along, someone who actually presented a challenge, he set things up to play a game with the blue hedgehog, complete with powerups of his own design (item boxes, shields, maybe even the rings themselves), and enemies, then waits and sees how well Sonic fares. Then he fights Sonic himself in a machine that has a built in weakness, and it's up to Sonic to exploit it.
Why else are the item boxes, which are clearly technology, there? It's even more obvious when you run across item boxes with Eggman's face on them, and opening those hurts you. Or the betting machines in the Casino night zone, or the fact that even Robotnik/Eggman's bases are pretty hedgehog friendly, what with Sonic sized tubes, and devices that Sonic can operate, or if you take Sonic CD into account, the fact that all the bad future levels are run down, even Robotnik/Eggman's bases. Without you, he no longer has a reason to keep them in good condition.
- In Sonic 3 and Knuckles, the ending where Sonic beats Eggman using his Super Sonic form instead of his Hyper Sonic one shows a Stinger where a singular EggRobo stands on top of a pile of his broken comrads with the implication that this is the exact same EggRobo Knuckles faces in his story. Since it's implied in-story that the playable Knuckles' story takes place after Sonic's, this means that canonically Sonic never once, turned into Hyper Sonic even in this game.
- Or maybe Knuckles' story is the non-canon one.