1) Everything about the finale builds to an amazing climax. Canons core make you use every character with unique levels, the biolizard is one of hardest bosses in a Sonic game and flying through space as Super Sonic and Hyper Shadow while Live and Learn plays is just perfection.
2) The boss fight is very standard but the sudden twist of a full body Mother brain fighting back and the baby Metroid saving you at the last minute, leaving behind the hyper beam and getting off the planet just in the nick of time is breath-taking