All this timeline and Amy talk has made me realize a couple things:
Sonic Advance was Amy's FIRST TIME being playable in a 2d game after her Sonic Adventure character arc. Despite this, Sonic Team considers this debut game UNIMPORTANT. Sure, there isn't much of a story being "Eggman is being a jerk, we have to stop him" but you know what other game has that storyline: Sonic the Hedgehog 1.
Amy Rose is not an important character to Sega/Sonic Team. She's in the shit list with Mighty, Ray, and the Chaotix. Sucks to be her.