I mean, Eggman now only blew up the moon, he also blew up their home planet in Unleashed, he enslaved an alien race to abuse their power
which ended up causing a rift in time and space that destroyed the space-time continuum by enslaving a Time Eater inside of the leftover tear, he's actually contentiously stealing the life energy from living things to power his robots ever since the original and to further extent in some titles, in Sonic CD he took over the world and Sonic has to prevent a bad future, if we go with outside media he's done a variety of depraved things in both the comics and the SATAM universe.
I actually like Bowser quite a bit, and he's a gem in the Mario RPGs, but I think Eggman has a lot more going to him and has been one of the consistently good things of the series. I think his fights are a lot more interesting, I think his personality is and he treads being comical and a serious villain better than Bowser, and works as coil much better to Sonic than Bowser does to Mario to make much more interesting situations. Also I do personally feel Eggman has done far more evil things than Bowser, but also more compassionate things, but it works because he has a more versatile character.
Sonic Shuffle was a weird game.
