UPDATE: The animator who made this video, Joel MacMillan, has pointed out in a comment on the video that it wasn’t meant to be used in Sonic Chronicles but was instead a personal project a couple of people at Bioware made in their free time and thus is not officially made by Bioware. He also said that he’ll see if he can find the fully scored sequence.
Turns out that Sonic Chronicles: The Dark Brotherhood was going to have an opening with some very nice looking 2D animation. Shadzter from the Sonic Stadium did some digging around and found a demo reel by Joel MacMillan, an art director at Bioware who worked on the game. The video contains some clips of this opening starting at 1:12. The animation made use of both screens on the DS, with stuff happening on both of them.
Why the final game didn’t have this opening isn’t known. Our best guess is that it’s because the stylistically it looks incredibly different from the game. It’s a shame, because it’s clear that a lot of work was put into making this.