If Chris wants to retcon any outside influences, he should start from his first fantasy girlfriend, Sarah Hammer. She did get written out of the continuity when she married William Spicer, but doesn't that already screw up the whole Anchuent Prophecy?
If he was going to retcon it, I could see him still using the Anchuent Prophecy plot, so I'd rectify it by replacing Sarah and Wes, and their transformation trinkets. I'd make it simply that, unbeknownst to Chris, and known only to the old man and Graduon, when Chris recieved the Sonichu Medallion, it created three other medallions to maintain the power balance, and counteract eachother. A Rosechu medallion, a Giovanni medallion and a Robotnik medallion.
An unknown sweetheart-to-be would get the Rosechu medallion, which gives her own Rosechu form comparable to Saramah, but Chris wouldn't meet her for a few episodes. Giovanni's medallion would make his Pokemon stronger, and Robotnik's medallion would increase the strength of his Robot Armada.
Giovanni would want Sonichu for his hybrid Pokemon qualities, and Robotnik would want him as a battery for Metal Sonichu, which he'd use to crush Sonic. Until Sonichu is captured, Metal Sonichu would be a pure robot running on Ring power rather than containing Sonichu as a battery.
Eventually, I'd have Metal Sonichu turn rogue on his creator and steal both the Giovanni medallion and the Robotnik medallion, having the effect of turning him into an Ultra mode, so it creates a nice bit of duality between Sonichu and Metal Sonichu, and would give them both an Ultra Mode for a final showdown.
It's just interesting how tight you can make the story with mostly just the Sonic & Pokemon elements, sans-trolls. When there's a troll in the story, Chris's mind breaks a little and he's so focused on killing the comic troll that he can't even make his story about Sonichu.
But hindsight is 20/20, especially when you don't have a sponge for brains.
