Eggman has only worked well as a VERY serious villain in SA2. He does not work as a serious villain otherwise.

People want Eggman to be this serious villain but Sonic is a franchise that is meant to run forever and be very flexible enough that many many different types of plots can work. Having Eggman be goofy the vast majority of the time makes it easier to justify his inclusion in loads of different types of plots.

If you want a serious villain make a new villain, Eggman can be dangerous but rarely serious.