I think pride is an acceptable flaw. I'd say a fatal flaw for a Sue is something like "he/she has gorgeous blue eyes, and the rest of the world hate him/her for not having brown eyes like them", if you get what I'm saying.
Eheheheh... it IS a weird idea now that I think about it. The whole idea was to basically have the Sue do his/her own thing while one of the characters on his/her bad side watch and fight as the whole world slowly falls apart.
Right now, I wanted to start the story with the Sue having one universe under his/her belt and stumbles into another world. Live the fantasy and take it with him/her.
TL;DR, typical Mary Sue story except from the "bad guys'" POV. Then again, fanfic is a bit... stupid in a lot of eyes.
It's not a matter of stupid so much as 'is this gonna come out interesting'. I don't personally see the appeal in reading a story that deliberately features a perfect villain, but presumably you know who's going to read this.
To be honest, I really like writing out random drabbles to blow off some steam. Heck, this is just supposed to be a throwaway fic. I think the idea is decent, but I'm scared to screw it up (partially because this would be my first impression here and fans are really elitist sometimes).
I'm fine with a parody Sue. I just want the character to come across as a Sue. Considering I want to tell a Sue story from one of the unaffected characters' point of view (namely the main characters from a certain series), trying to sell the idea to audience would be a bit difficult.
Unfortunately, unless the Sue never pays for it, having a fatal flaw is something most mary sues lack. However, I think one of the biggest signs of a Mary Sue is how the other characters react to her (or him). Nobody is indifferent to a Mary Sue. Everybody loves or hates her. If your character does all the damage by himself, is almost invincible, and nobody is neutral to him, I'd say you got a Mary Sue. Sue names: Marcus (Warlike) Aaron (Strong) Kana (Powerful. It's a Japanese unisex name. According to Mary Sue tests, Asian names for non-Asian characters are sueish traits.) The Mary Sue character I made by accident when I was 12 name was Estella (Star.).
So what you're saying is that even if most of the universe hates her/him, if she "wins", it would count against (or in this case, for) her/him, right? Taking a worst case scenario: Sue gets the girl, then annihilates a bunch of overpowered characters in almost an instant.
One of my old OCs that I keep tweaking is Cyrus Soldati (sun; soldier). Yeah... he was definitely a Mary Sue when I came up with him (Pokemon fanfic, natch).