After sleeping on it, I think I've got the current Modern Sonic timeline down. There aren't any plotholes or shit like that. Games that got excluded from Sega's official timeline fit into place without issue. The only revelation is yeah, Sonic Advance is a remake of Sonic Pocket Adventure. From the first boss being an Egg Hammer to the Last boss being the Egg Mobile with Hands, its clear that Dimps & Sonic Team were redoing the SNK stuff.

Modern Sonic Timeline

Sonic the Hedgehog 4
Sonic Adventure
Sonic Shuffle
Sonic Adventure 2
Sonic Advance
Sonic Advance 2
Sonic Pinball Party
Sonic Heroes
Shadow the Hedgehog
Sonic Battle
Sonic Advance 3
Sonic Rush
Sonic the Hedgehog(2006)
Sonic Riders
Sonic Rivals
Sonic and the Secret Rings
Sonic Rush Adventure
Sonic Rivals 2
Sonic Riders Zero Gravity
Sonic Unleashed
Sonic and the Black Knight
Sonic Colors
Sonic Generations
Shadow Generations
Sonic Free Riders
Sonic Lost World
Team Sonic Racing
Sonic Forces
Sonic Frontiers
Sonic Dream Team