As a writer, one of the main issues I suffer from is having a great idea for a climactic or just really cool moment in the middle or end of a story, and rushing the beginning to get there. I honestly think that's maybe what happened with Sonic 06-as a whole, not just the story. Like, Sonic running on the side of a waterfall at Mach 2 with light shining down from the end of the tunnel, made up of more waterfalls and Elizabethan architecture, is my favorite moment of Sonic spectacle in-game, hands down. But when I consider just what led me to this moment (a terrible story with a lot of filler and not enough substance) and the actual gameplay itself (Sonic dies by tripping on rocks and can't even move in the air), it becomes less enjoyable. Those beautiful high speed sections of spectacle, as well as some of the better-looking cutscenes, are some of my favorite moments in Sonic history, but what comes before or after those moments is just a lack of good buildup.
Though this is only one problem of many-the rushed release date and internal issues also didn't help.