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In Adventure 2, we discover that Eggman is merely the presumably latest scion of a long line of geniuses, and was personally deeply inspired by his grandfather, Gerald Robotnik. Professor Gerald was hailed as possibly the greatest mind of an age, and considering the similarity in his and Eggman’s signature mustaches, it’s entirely possible even as an adult Eggman styled himself in his grandfather’s image.

Gerald was the lead researcher on the ARK, and the mastermind behind Project Shadow. He was searching for a cure for his granddaughter, Maria’s, illness, but largely optimistic about the way that his research would benefit everyone living on Earth. (It is never made clear Eggman’s relationship to Maria, if they were cousins or siblings, but considering Maria lived with Gerald on the ARK, and Eggman implies he admired Gerald from afar, whatever their relation, they were likely not very close, especially as Maria was personally close to Shadow and Eggman didn’t recognize him by name or looks.)

However, ARK was shut down due to suspicion regarding the project and Gerald’s covert dealings with the tyrannical, conquering alien Black Doom. As a result, there was a raid made on the ARK to seize the results of Project Shadow and take Gerald prisoner. This raid was horrifically botched and turned into a massacre, during which Maria and Shadow fled, trying to get to an escape pod, but Maria chose to seal and launch Shadow’s pod first, defying the orders of a pursuing soldier to do so, and was fatally shot. This utterly destroyed Gerald’s faith in humanity and sent him down a very dark path, eventually putting a “ghost protocol” into the ARK that would cause it to crash into the Earth and kill everyone, manipulating both Shadow and Shadow’s prototype, the Biolizard, to do so. This protocol, and Shadow, remained dormant for fifty years until the latter was awakened by Eggman.

During Last Story’s final cutscenes, Eggman reveals that he was inspired to become a scientist by his admiration for Gerald, and was seemingly equally embittered by the botched massacre, though he’s shocked and outraged by Gerald’s ghost protocol. This is not remotely the first or only time Eggman has been shown to be deeply offended by the notion of destroying the entire world and he’s been shown to be either snide towards or make significant countermeasures to entities such as Perfect Chaos, Solaris, Eggman Nega, or Black Doom, who are purely interested in destruction for destruction’s sake.

Eggman has also made many allusions that he seeks to build a city that he sees as a utopia, and, when he’s actually able to achieve his dream in Sonic Unleashed, it’s worth noting that Eggmanland looks overwhelmingly like an amusement park rather than a sinister police state like his SatAM self does. Eggman’s amusement park in Colors also is very bright, colorful, lively, and seemingly genuinely designed to entertain, to the point of recording and making a bunch of PA announcements that don’t make sense while the park isn’t even open yet and he, Sonic, Tails, the wisps, and his cadre of robots are the only people there.

So here’s my take on Eggman’s objectives:

He’s deeply embittered with the government and assumes they can’t be trusted for anything because of the ARK massacre and GUN’s following capture and execution of Gerald. Given this was fifty years ago, Eggman could have been a child at the time, which would make this even more traumatic.

Eggman’s also just plain bossy. He’s a genius, he’s charismatic when he wants to be, and he’s also a pretty good strategist, as he’s the one who primarily coordinates everyone’s joint efforts during Last Story (he instructs everyone during their respective missions with the exception of his own, when he takes input from Tails), the problem is, he is keenly aware of this and it has gone straight to his head with like no stops.

So naturally Eggman’s response to any kind of beef with authority is that everything could do so much better with him in charge and the nature of his projects betrays both his glaring ego and, buried in the supervillainous ham, a genuine desire to make something that will make people happy.

It’s also worth noting on many occasions Eggman is shown to have a surprising amount of respect for Sonic considering how much he gripes and calls him a pest or a rat- the extent depends on continuity. In Adventure 2, he’s comfortable potentially dispatching Sonic, but, gives a moment of solemn introspection in Sonic’s honor, and in Sonic X, when Sonic appears to be gone and never coming back Eggman unsubtly launches full petty theatrics in mourning. 

In general, though, the impression that comes across is that Eggman can respect a lot of the things Sonic stands for- which, combined with how many times they’ve worked together or Eggman has appeared to set Sonic up as a countermeasure if his habit for wantonly harnessing ancient gods gets out of hand, would suggest they’re on at least as honorable terms as old school superhero nemeses.

And likewise, we see our heroes throw Eggman a bone now and then- such as when Chip (who’s not familiar with Eggman) suggests they need to quickly save someone Eggman has held hostage because he’s hungry, and Tails immediately reassures Chip that Eggman must be feeding him... and sure enough once they find the guy, he’s unharmed and unfazed enough to be basically complaining about the room service because the specific kind of sandwich he requested doesn’t live up to his standards.

In short, I’ve personally read Eggman and Sonic’s rivalry as an Order vs. Chaos divide, with Sonic representing chaos, and Eggman representing order. So that’s Eggman’s ultimate goal- not harm, not destruction, not even his ego, as much as he thinks there’s a better order the world could conform to, and who better to know what the world needs than a certified Robotnik genius? He had a keen personal lesson in the problems of the existing systems, after all.

I think Sonic and Eggman both want a better world. Their disagreement is how to get there- Eggman thinks everyone should shut up and listen to him because he knows what’s going to help and also, well, you can’t make a utopia without cracking a few eggs, or kidnapping a bunch of small animals and using those adorable little buggers as robot batteries.