I think we need a brand new canon for Sonic, since the current one is only headed for more disaster, and the Archie Comics canon isn't faithful to Yuji Naka's original concept. So we need a brand new series of Sonic games, titled Sonic: Mobius Legend.
Essentially, this will be a seven-part series which follows Sonic from his earliest heroic days to his moment of truth, where he saves the world from the apocalypse. No spin-offs or continuation of the series. Just 7 chapters, progressing in linear order.
In case you're wondering, "why seven?", the answer is that the story is heavily centered around the Chaos Emeralds. Unlike previous games, where the emeralds have been reduced to shiny trinkets that give you superpowers for a short time, the emeralds are truly rare in this series. In fact, the emeralds are so difficult to obtain, that one emerald is discovered per chapter.
Anyway, in each chapter, Sonic races through all the zones to face off against Dr. Robotnik in the end, a la classic gameplay. In each chapter, Sonic learns new moves which become essential in later chapters. As such, gameplay will become steadily more difficult through the series.
The story itself is essentially a retelling (not a complete remake) of the original story in the Genesis games and beyond (to a point).
Chapter 1: Sonic meets Dr. Robotnik and learns about his plans to roboticize all of the citizens of Mobius. The Blue Emerald is discovered in this chapter.
ZONE 1: Azure Lake - Requisite Tropical level.
ZONE 2: Marble Palace - Ruins submerged in the sea.
ZONE 3: Sky Highway - A highway suspended over a city. Similar to Star Light.
ZONE 4: Pinball Park - Pinball level.
ZONE 5: Haunted Mine - Similar to Mystic Cave from Sonic 2.
ZONE 6: Lava Powerhouse - Lava and machinery. Pretty self-explanatory.
ZONE 7: Cybernetic City - Robotnik's city and fortress.
Chapter 2: Sonic finds Tails, and the two become like brothers. When he learns that Robotnik killed his parents, he swears that he will see to it that Robotnik is killed.
ZONE 1: Emerald Island - The requisite Tropical zone.
ZONE 2: Mystic Forest - Towering trees and thick vines create a unpredictable path of twists and turns.
ZONE 3: Casino City - The high-rolling Las Vegas style city.
ZONE 4: Dust Valley - A barren wasteland with sand as far as the eye can see.
ZONE 5: Underground Palace - The ruins of some ancient civilization. Will some mysteries of the Chaos Emeralds be revealed here?
ZONE 6: Mechanical Metropolis - The two make their way across the oil-polluted ocean and invade Robotnik's factory.
ZONE 7: Aerial Pursuit - Sonic and Tails crash the flying warship. Then Robotnik escapes to the Death Egg, but Sonic follows him. The final showdown is included in this zone.
That's all I have for now. If you feel like expanding on the idea, feel free.