Disclaimer: I know enough about the "Mary Sue/Gary Stu" trope to know that even it's mention is enough to insight angry comments, a sea of downvotes, and internet rage galore. I am asking kindly that you leave your strong opinions on this trope at the door. I am looking for advice on writing with these types of characters; no more. I am fully aware that the idea I am about to present does give a negatively skewed view of this character type, but please try to keep an open mind if you are a fan of characters commonly associated with this trope. With that out of the way, let's begin.
Recently, a friend of mine, who helps me with brainstorming, pitched me an interesting story idea. The basic premise is that the archetypal overpowered and shallow teenage group of heroes (like something ripped straight out of a self-insert fanfic) have smote the archetypal evil emperor as always. But instead of peace returning to the land, there is a massive power vacuum created, resulting in a bloody and violent civil war (trying to commentate on how these sorts of characters IRL would just make the problem worse). The story follows one of the factions in the civil war that directly blames the "heroes" and their attempts to hunt them down for what they did. I'm planning to have this be something of a commentary on these types of protagonists complete with meta references and all ("I can hit them! Their plot armor is too thick!).
Now with that exposition dump out of the way, how should I write the Sue/Stu villains? I had an idea, but I'm not super sure about it:
The Sue/Stus are, like the characters they are parodying, completely and blissfully unaware of their shortcomings and are self-righteous jerks (going as far as to ask for free stuff just because "they saved the realm"). They never see the error of their ways throughout the story, and they demonize and oppress people who don't like them (even if they are non-violent), claiming that they are evil supporters of the old empire or something like that to justify their extreme actions against them.
The idea is that the story shows the harm that comes with the "I'm the hero so I'm perfect!" mentality (as well as these types of characters as a whole). I'm worried that if I make these characters a bit TOO overpowered and self-righteous, the message will be lost because the characters are too ridiculous. I'm also worried about toning down the "Sue/Stus" won't make them "Sue/Stu" enough (not to mention that my point kind of is to demonstrate how ridiculous this character type is). Also, some peoples' definition of a "Sue/Stu" has the offending character take over the story to the point where every little thing is all about them. This is a problem because I'm planning to try and flesh out my protagonists to give an example of heroes with reasonable flaws and abilities for the setting. Making the protagonists like this drags attention away from the "Sue/Stu" characters, so some might argue that they aren't the center of the universe; and therefor aren't "Sue/Stus" (thus undermining my entire purpose).
TL;DR: I don't like the "Sue/Stu" character type so much that I want to write a novella about it, but I'm so bad at writing that I'm not even sure how to "Sue/Stu" correctly.
I would appreciate any advice on how to make these characters work. If you disagree with the way I'm going about this topic, you can feel free to leave a comment, too. No matter what you intend to do, thank you for your time. Have a good day!