Though, I'd like to see a sequel (and hopefully include Silver and Blaze, respectively), I doubt it will.
Like you said, they seemed to be pointing to a sequel, but it seems BioWare have blow their chance it making a sequel for it, and it is very unlikely Sonic Team will pick up after it.
Making Sonic Chronicles; The Dark Brotherhood, a "what if" game, similar to Sonic '06. Except Ivo wins for a change.
Which reminds me...I have "Sonic Chronicles II" game in progress, that was mothballed, due to recent depression...I will resume it now.