I've had one idea lingering in my mind, not sure if it's good though.
It would follow the original comic somewhat, except for a few differences:
1.) In the first comic, It doesn't show that pikachu turned into Sonichu, although it implies it (more on this later in the post). He doesn't fight Perfect Chaos, rather, he wakes up in a forest in the kanto region, with no memory. After a few scrapes and incidents, Sonichu gets taken in by Kel and Rosechu, who then name him Sonichu.
2.) All the Chus possess more character. Punchy is a guy that tries to be asian based on being raised in a dojo, only to come off trying too hard. Wild is more unpredictable, seeing as how he was raised away from civilization. Magi-chan would have a massive ego, and is cocky as hell, believing that he could take on all the PVCC with no help. Bionic is actually a Mobian android designed to be loyal to Chris without question. Although Blake would still join the Chaotic Combo, he would secretly be working for PVCC. The list goes on and on.
3.) I would use real-Chris in the place of the comic one. In many of the episodes he will try to make the plot all about him, such as the Anchuent Prophecy (which is just another of Chris' toys made from his team of scientists, more on that later). Most of Chris' wants and hatred against homos isn't taken seriously unlike the comic, however he has enforced homophobic laws, much to Magi-Chan's displeasure.
4.) Sonichu has more morality, being a creature that doesn't quite yet comprehend why he's designed the way he is. With that said, he constantly questions and chews out Chris regarding his stupidity. Some of the plot would revolve around Sonichu trying to figure out where Sonichu's come from.
5.) Get rid of Sonichu and Rosechu's children. Just no.
6.) More villans. Not only do we have Walsh controlling PVCC, we also have a secret person, who is called S, that works with Mary, almost like her boss. Sonichu and S would battle on several occasions, where Mary was, S wasn't far behind. Mary herself would have a more complex backstory, haven't completely thought of one yet though. Their attacks would be more focused on Chris rather than CWCville itself.
7.) Include more references to Pokemon and Sonic, seeing as how they are the same universe in this shit. I would also get rid of other references such as Sailor Megtune and the Yu-gi-oh crap.
8.) After the execution of the Asperpedia Four, Sonichu begins to lose his faith in Chris, starting to feel contempt for him. Afterwards, he asks Chris if he found out how to defeat PVCC while he was in the future, only to lose his last bit of patience when Chris tells him that he found a "cure" for the homos and that was the most important thing. Sonichu decides to flee CWCville at Blake's suggestion, to clear his head. In his journey he fights S one last time. In the fight, he manages to rip off the cloak that surrounded S, only to jump back in shock. S was Sonic the Hedgehog. In Sonichu's shock, he didn't realize where he was going, he ran into a cliff, knocking himself out. He wakes up in PVCC's headquarters, and to his surprise, he wasn't tied up or anything. Sonic enters the room and explains everything to Sonichu. Turns out, Sonichu wasn't created from the Perfect Chaos monster, he wasn't even there! During the battle, the monster killed Amy right before Sonic's eyes. From that battle, Sonic came to the realization that his heroic antics placed his loved ones in danger. He didn't want to fight anymore. Years later, he met Bob Chandler, mayor of CWCville. They both knew that their world's needed a hero. So with Sonic's permission, Bob hired a team of scientists to clone Sonic, thus creating more heroes.
During the project, Bob passed away, leaving CWCville to his son, Chris. Chris takes over the project, demanding that they add in pokemon DNA into the mix, based off his comic series he's been drawing. His plan was to use them as "his personal heroes" that aid him in fighting off the homos and anyone who trolls him. Sonic attempted to stop Chris, but it was too late. The creatures were now tainted with pokemon DNA. Sonic's attempt however, was not in vain. He managed to steal the infant clones and scattered them all over Kanto. Afterwards, he joined Walsh in attempting to take down Chris and his tyranny over CWCville.
Sonichu, upon hearing this and through much thought, made the decision to join Sonic and the rest of PVCC to stop Chris. While all this happens, Chris lies to the Chaotic Combo, saying that they brainwashed Sonichu. Now Sonichu has to team up with Simonchu, Silvana, Sonic and the Jerkops to take down his former friends.
Like I said, this has been an idea forming in my head for a bit
