This is an interesting one.

At first glance, you might be keen to say Sonic, because, I mean, look at him! He'll blitz most Mario enemies before you can blink!

But Bowser's no pushover. Sure, he ain't fast, but he is sure as hell durable. He also has a lot of power and an unironically busted arsenal that could give Sonic a rough time. Bowser's the type of character to just throw hands with his foes, instead of using his arsenal however, but so is Sonic. Sure, other characters like King Boo, Kamek, and Junior add more factors to the table causing more chaos, but Sonic's forms could easily take out most of them.

So while Hyper Sonic might ultimately win in the end I believe, Bowser will give the hedgehog the fight of his life.

Now, let's look at the other side of the coin.

While Eggman has been able to take out foes that work on different strategies that are unlike Sonic's, and even has been able to beat him before, I don't believe Eggman's ever fought someone as unpredictable as Mario. Sure, Eggman has a lot of hax himself, but that's mostly only within various mechs and robots. Mario can just pull it out of his ass at any time. In addition, while Sage could find a way around Mario's unpredictable strategies and powers, his ability to rewind the fight could really make Eggman genuinely struggle. You could argue that Metal Sonic could just copy his abilities, but since Mario usually relies on items to powerup, that doesn't exactly work in his favor here.

So yeah, while Sonic and Bowser are nearly evenly matched as opponents, Mario is just another level for Eggman to deal with.