Playing though it for the first time, thought I should start dishing out my plot hole-filling theories. DISCLAIMER: I DO NOT CLAIM ANY OF THE FOLLOWING TO BE OFFICIAL CANON. ALL REFERENCES TO THINGS BEING “CANON” OR NOT ARE MADE WITHIN THE CONTEXT OF MY VERY OWN FANON. Think about it like Adventure, with all stories taking place simultaneously: Not all four characters canonically do all seven zones: Cream starts in HC, Tails in IP and Knuckles in TB (they chase Sonic through all the zones that come after their associated boss fight (that's why only Sonic's story features the others within boss fights: they're already chasing Sonic)). Cream, Tails and Knuckles don't fight the bosses or get to XX (Eggman is already in the next zone, plus he already has enough having to build two of each boss). Apart from that, my own personal opinion on the handheld series: I consider it a different canon from the console games so I can retcon some Special Stages out by saying Sonic had all the Chaos Emeralds since Cosmic Angel's Special Stage until he landed in the Sol Dimension, because otherwise Cream, Tails and Knuckles would've caught up to him in Advance 2, he would've had to backtrack in Advance 3 and he definetely would NOT have reached Dead Line's boss arena right after Blaze. Colors' are OK but I know nothing about Lost World 3DS and I consider Generations to be non-canon anyway. With that, I conclude this theory. Lots of streched interpolation and non-canonization of part of the game, but I believe it's best to do this and not something that could reach '06 levels of convolutedness.
I don't see what you're filling in? The game has a very loose and barebones story from what I can remember, there likely wasn't as much thought put into it as you're putting forth here. Additionally I can't speak for others but I cannot tell the Sonic Advance 2 names by the two-letter abbreviation. When you're making a forum post, please take the five seconds to type the full level name out at least once.
Sonic Advance 2 has an extremely intricate plot and a ton of hidden depth. You're close to the truth. Keep digging.
While I don't really see the point of this thread, the Advance games certainly do have stories. Advance 1 was... Well Eggman is building a rocket to do evil space stuff! :specialed: Advance 2 is all about saving Vanilla Rabbit, Cream's mom. Advance 3 is a direct sequel to Sonic Battle where Eggman has almost perfected his technique for building a Gizoid, the end result being Gemerl. Game happens and then Gemerl is now a butler to bunnies. :v: Edit: Oops, wrong quote.
Yeah, Advance 3 felt more like the Genesis games in terms of plot progression. Plus Gemerl rocks my socks. Here's an actual plothole though for Advance 2. We never found out exactly how Eggman tricked Knuckles. Instead after the Knuckles bossfight (trigger warning: It was the wheel/donut boss), Sonic's all like "You wally, Eggman tricked you again!", but we never knew any more than that. I mean, imagine my 14 year old self not being able to sleep that night. "B-but what did Eggman say to Knuckles... to get him into... that fucking Donut boss that I can't stand...." Really makes you think.