For the first boss fight in Episode 2, the stone columns from Aquatic Ruin Zone rise from the ground. Then Eggman reveals a giant plant-machine, and smashes the columns, indicating he's finally getting serious and not using boss rehashes!
Eggman's second boss in Oil Desert Zone. His Egg-O-Matic sprouts a large electromagnet and assembles a giant robot made of scrap metal in seconds.
The fight against Metal Sonic on the roller-coaster ranks as one of the most intense Sonic boss battles ever, where Metal shows up still smarting after losing to you in Sonic CD and is determined to make you hurt. And goddamn if he doesn't throw everything at you to do so.