Well, yeah, but I don't think that's Eggman's primary goal this time, as it was in Sonic 1. Revamping animal-powered badniks is merely one mean to achieve his goal of eliminating Sonic once and for all.
Understand, though, that this speculation is solely based off a pretty liberal interpretaton of Eggie's character info on the website. Also, I just think it would be hilarous if Sonic totally squashed Eggman's ambitions in Sonics 1 thru Knuckles, so Eggman goes haywire and throws his remaining resources into attempting to kill that one damned hedgehog.