I've been reading your list of things you would change if you could restart TOTMIS, and honestly it makes me realize that spite is not always a good motivator when it comes to fix-it fics. Sure it may lead you to fix the mistakes of canon like it's supposed to, but it may also cause you to make new mistakes as well.
I have a bit of a mixed take on that.
Don’t get me wrong, I 100% agree that you need more than spite when writing a long, on-going story. If that is your only motivator as a writer, you’re going to burn out pretty quickly. For most of TOtMiS, the chapters mostly focused on being an AU version of season 3 episodes to accommodate for the ship and story beats that were present due to the changes. That made outlining for those parts of the story much easier.
But later parts, like “Horror Head” were much more difficult. And that’s because at that point, I couldn’t just pick a season 3 episode to draw from and write in response to it. I had to write in response to what I set up, which ended up being a lot more than I realized. (Note: yes, you should be writing in response to what you set up in general, but that’s beside the point).
It also didn’t help that I hadn’t planned on writing a long series - “Silence Can Be Beautiful” was originally a one shot written because I loved “Silencer” so much and just wanted more of it. And then the rest of season 3 started to happen, and the rest is history.
That being said, I don’t want to discount the value of venting frustrations via fanfic (to an extent). Certainly, I’d rather people vent their frustrations that way over more toxic means, like harassing people for not agreeing with their opinions. And if someone stumbled upon their fic, doesn’t like or agree with it? They can just block or drop it and move on.