Yeah. On the topic of Bowser and Eggman, they also have completely different goals. Eggman wants to build a city, and Bowser wants to rule the universe. Someone's thinking big.
Also, don't forget that Eggman has 'boasting' problems. He gloats about stuff in the first few minutes of putting his plan into action. It's almost like he might be in Sonic's house yelling "HEY, SONIC, I'M GOING TO USE THESE TO TAKE OVER THE WORLD SO DON'T MOVE!!!!!!!!"
And someone also has the brute force to back it up.
Well, there is a similarity: They want to smash, crush, pound, and destroy a pesky little hero who is way more powerful than they have any right to be given what they are.