When it comes to making a Modern Sonic game timeline, there isn't any plotholes or inconsistencies outside of Eggman Nega being either from the Future or Blaze's dimension. The biggest question is with Pocket Adventure and Advance: "Is the later a remake of the former?". We may never know for certain.
Modern Sonic Timeline
Sonic the Hedgehog 4
Sonic Adventure
Sonic Shuffle
Sonic Adventure 2
Sonic Advance 2
Sonic Heroes
Shadow the Hedgehog
Sonic Battle
Sonic Advance 3
Sonic Rush
Sonic the Hedgehog(2006)
Sonic Riders
Sonic Rush Adventure
Sonic Riders Zero Gravity
Sonic Unleashed
Sonic Colors
Sonic Generations
Shadow Generations
Sonic Free Riders
Sonic Lost World
Team Sonic Racing
Sonic Forces
Sonic Frontiers
Games that need placement
Sonic Advance
Sonic Rivals (No Sonic Channel Page)
Sonic Rivals 2 (No Sonic Channel page)
Sonic and the Secret Rings
Sonic and the Black Knight
Sonic Pinball Party
Sonic Dream Team
Games that are not canon
Sonic Runners
Sonic Runners Adventure
Sonic Dash
Sonic Jump
Sonic Chronicles
The Murder of Sonic the Hedgehog (No Sonic Channel Page)
Sonic Pocket Adventure (No Sonic Channel Page)
Notes
Sonic Pocket Adventure and Sonic Advance are eerily similar.
Sonic Rivals is hard ignored by Sega to the point of not even having Sonic Channel pages.
Mobile games like Sonic Runners are not considered.
Sonic Chronicles is missing due to legal issues.
The Murder of Sonic the Hedgehog disqualifies itself (see its steam page).
