I'd go down the gritty reboot path, more or less removing any specific references to copyrighted materials and real people (barring Chris and his family), though their character archetypes will remain to an extent (mostly troll depictions though as well as some of Chris' depictions). Rather than the various Sonichus being based off of Sonic and Pikachu, they will be genetic experiments, particularly abusive genetic experiments on animals. Any of the crazy ideas here could only be presented as incredibly dark, otherwise you really couldn't do anything with them and they'd be too ridiculous for a comedy.
While the Sonichus (for a lack of a better term, they wouldn't actually have a specific species in the story) would be generally good-natured, Chris would be a horrendous tyrant, running CWCVille as a dictatorship. The reason for this would be having absolute power like in the comics, changing the currency to a senseless denomination, setting up offices in the central mall, mandated Dating Education, no sense of economy whatsoever, government spying, mass murder, rampant racism and bigotry, and prosecution against those JERKS adding to the Infinitely High Boyfriend Factor. The Sonichus would work together to restore the country to what it used to be.
It would start out with Bob having control over CWCVille (which would have a different, more sensible name), being a prosperous king in an executive constitutional monarchy, keeping the country in good economical shape, the people extremely happy, and everything going great. Both Christian and Liquid Chris (under the names Ian and Christopher respectively) are his sons, however because Liquid is older, he is in line to inherit the throne. Chris, to put it lightly, does not like that one bit and goes out of his way to vilify both Liquid and Bob. Through his family's wealth and name, he is able to form a resistance, though it's closer to a cult, and starts a research program to create a superior life form. Chris has drawn in his notebook since he was a kid and is a massive enough idiot with a massive enough ego to think that it's actually prophetic and can be made through genetics, thus starting the search.
The problem here lies in that he is stealing dogs to research on by sending members of his resistance to steal them. This is how the main character gets involved, who really isn't based on anyone, though I suppose I could make an argument for Wes Iseli (though renamed Andrew Leon) since he's a rival to Chris at a few points, I guess. He is a veterinary researcher which explains his interest in what's happening to all these dogs and has his dog stolen by Chris' resistance. He starts a relentless search to find his dog. The same thing happens to Kel (who actually has a purpose in this story), whose dog has been stolen by Chris as well.
For better or for worse, Chris' genetic experimentation actually works, turning Andrew's dog into the parallel for Sonichu and Kel's dog into the parallel for Rosechu. However, the scientist doing the research (who is based off Troll!Bill the Scientist) hates this research and breaks out Sonichu and Rosechu (they aren't created at the same time). After this, Chris starts a coup on Bob. Seeing this, Bob sends away Liquid to safety and puts up an extremely good fight against Chris. However, Chris kills him and succeeds in taking over the kingdom.
After this, he turns it into CWCVille starts up on the insane policies and making multitudes of Sonichus (including the parallels for the Chaotic Combo). If I went into detail on tons of the plot points I'd be here forever. But one is closing down all public education for Chris' mandated Dating Education, where women are forcefully put into relationships with single guys. This angers the dean of the major public college of CWCVille, who is a parallel to Mary Lee Walsh (troll!Mary Lee Walsh), for multiple reasons. Eventually, Sonichu reunites with Andrew, Rosechu finds Kel, Kel and Andrew find each other. They find Liquid, who wants nothing more than to avenge his father's death and restore order, and they find Mary Lee Walsh, who wants things to go back to normal. They all form an alliance to take down Chris' empire and put Liquid in the throne where he rightfully belongs to restore order and find justice.
