There is an extra scene at the very end of the credits of Shadownpicking up one of his inhibitor rings off the floor, which Shadow survived, that also means Eggman potentially survived too, probably by Shadow using his chaos control to grab Eggman and warp him out just in time before the Eclipse Canonn's core explodes. Sonic 4 is basically leading up to Sonic Heroes, the next Knuckles Season was announced to have Chaotix, the writers are still figuring out if Shadow's spin off should be a movie or series (which potentially could introduce Team Dark). Everything leading up to Sonic Heroes, and in Sonic Heroes, Eggman was in hiding the whole time while Neo Metal Sonic pretends to be Eggman. There is definitely a good chance that Jim Carrey will return as Eggman.