You already know what Sonic & Mega Man: Worlds Collide made to the comics, the Ken Penders problems and Sonic Team restriction made to the comics, but let's imagine an alternate world where the second thing never happened, the third is not that strict and the reboot was made for other reasons. Like, to make it easier to enter for the new readers, reimagine some concepts and introduce new others.

Something more similar to the Marvel's Ultimate universe, basically post-Super Genesis Wave but better. I call it "Genesis Universe"

Some of the ideas I have for how it would be:
-Remember Sonic Armageddon, where Mobius ended being destroyed? Well, here also happens, but it's not the ending, it's only the beginning; generations before Sonic and company, Mobius has been destroyed (Eggman has nothing related to this) and the Mobians had to migrate to Earth. The reason of the choice was because, in this alternate universe, Mobius and Earth are different planets, but relationship between Mobians and humanity is much older than it looks.
-Sonic is a rookie hero in search of answers about his past, part of the third generation of Mobians raised on Earth along characters of similar age.
-Eggman is a human supremacist who hates Mobians just for be in his planet.
-Tails' double tail condition is an effect of a mutation.
-Other SEGA franchises would be part of this universe, having his own comic series, making a shared universe. The unique one I found hard (nearly impossible) to introduce is Project DIVA.
-Obviously, some arcs would be made to promote upcoming games.

I have much more in mind for this, but I can make a whole encyclopedia about it. Everything would start with Genesis Sonic #1 (~2013), and would end with an event at the style of DC Rebirth: The Genesis (~2033). Here, it would be revealed that the remnants of the previous universe had not died with the Super Genesis Wave that originated the new one, but survived in a sleep state, being the main premise of the crossover event.

Everything ending with another Super Genesis Wave, and the phrase "it all starts with a Genesis."

Answer in the comments: How would you make it?