Hmm, seems despite all of the constant worry and panic, Amy is going to make it into the game after all! It was revealed in an IGN Insider interview with SA2 director Takashi Iizuka:
IGNDC: Will we see any of the old characters from Sonic Adventure?
TI: Uh… good question (laughs). Amy is very well involved in the story but unfortunately she’s not playable.
Well, there you have it!
Source: The Moogle Cavern