The levels and bosses are all in chronological order in the main Generations, so unless they only want to use content from SA2 and Shadow's game then Mephiles would be the most recent villain for Shadow.
Doesn't mean he's going to be the final boss though, or even in the game at all. 06 may have been important for Shadow's character but I don't know whether they'd be willing to bring Mephiles back. Then again, I never expected to see Black Doom again either.
