If we are talking purely hypothetical, I'd say reboot and starting fresh really is the best way. Too many loose ends and baggage. Tell each story one by one and have a plan and way-out for characters. There seem to be a lot of Sonic characters that gets introduced in a game, have their arch completed by the end of said game, and then just appear in the next game without any real purpose. Take my boy Knuckles for example. Dude was introduced as a guardian of the Master Emerald. In early stories like S3&K, SA1, SA2, they had to inert the Master Emerald in order to get Knuckles involved the story. But from Heroes on, no one knows or cares where the Master Emerald is. xD I found this old Sonic paperback book from 1995 written by Michael Teitelbaum on eBay. It re-tells the events of Sonic 3&K. It has a good solution for Knuckles imo. In this book, Angel Island is constantly dimension hopping and only appears in our dimensions every few years. At the end, the Master Emerald is stolen back from Eggman and returned but Knuckles is off the island when it dimensions hops again, leaving Knuckles stuck in Sonic's dimension. This gives an actual reason for Knuckles to start participating in stories without having to involve the ME, cause it's stuck in some other dimension somewhere! Just an example, but stuff like. Simple but effective ways to keep the continuity going but without getting to messy.