Kids' shows still eventually end, though, and Sonichu 10 ends an awful lot like a kids' show would. Mary Lee Walsh and the PVCC are clearly set up as the biggest villains, and the ultimate obstacle to Chris accomplishing his Love Quest. Defeating them is as final as Sonichu can get.
Kids' shows end not because there's anything in the genre that calls for a final resolution of the plot. Kids' shows are first and foremost commercial enterprises; the plug on one is pulled when it's no longer considered profitable. Seeing that Sonichu doesn't need to pull a profit in order to continue, there's no reason for Chris to stop. And while your description of MLW's role in the plot is correct for Issue 9 and 10, I don't think that Chris planned for her to have such a major role in the comics from the beginning of the series. In many issues her influence is not felt at all.
The fact of the matter is that, while Chris claimed he had a "second season" of Sonichu planned, he never divulged real details beyond that \M/ETAL Sonichu would return, and since he was so handily defeated at the end of his first appearance, making him the True Ultimate Villain wouldn't be likely. My theory is that Chris didn't actually have any plans for the second season, because he'd wrapped up the story so thoroughly.
Chris not making plans for season two is jut OPL being himself. The plot of season one didn't advance according to some kind of a plan, but according to Chris's whims at the moment he was writing. It's pretty clear that when Chris was just beginning to make season one (i.e in Issue 0) he wasn't planning for it to end the way it did. There's no reason Chris can't make season 2 in the same way if he wanted.
Besides, the return of Metal Sonichu was not the only future story Chris talked about. In
this video for example he mentioned a couple of other future stories. In the Jackie emails he mentioned that he had a backstory for how Robbie became a cross dresser, and he also had plan for a future
Blake episode. That's enough plot to give season 2 its start, and from there on the series can continue based on whatever bullshit comes into Chris's mind.
As for Metal Sonichu not being strong enough to serve as an arch-villain... Have you seen the last fight between CWC and MLW? She was defeated basically just as easily as Metal was. Chris doesn't like villains who can actually threaten his designated good guys, meaning that Metal is a fine villain by Chris's standards.
Chris had already constructed the Sonichu/Mary Lee Walsh mythology long before he ever put pencil to paper. He integrated the trolls, sure, but as minions of PVCC and other lesser villains.
Again, MLW was overall a relatively minor villain in Sonichu and in many issues she's overshadowed by another villain. For example, if one does not read Sonichu beyond Issue 6 he could easily be fooled into thinking that Reldnahc was about to become the series' arch-villain. He has new super powers, has becomes more evil, rebels against his own father and leader of his organization, and he also plans on conquering the world...
Chris's concept of MLW being the queen of all the evil that inflicts him has changed. Nowadays, he sees Megan and Snyder as the main architects of his torment. The current struggle Chris is facing (in his mind) is about much more than finding love; now he has to deal with a non-stopping onslaught of vicious trolls, whose only motivation is pure sadism as an end to itself.