Jerk Sue, Anti Sue and Villain Sue to realize that even a character with flaws can be a Mary Sue.
It has more to do with how the writer deal with those flaws. If the flaws don't cost anything to the character, aren't detrimental to the character and the other characters never call him/her out on them, then that's a pretty good Sue sign.
Like if a character is hot-headed and loses his temper easily, and that causes one of his pokémon to run away and stop trusting him, or one of his travelling companion to get into an argument with this character and later join with the villain, then it's not a Sue. If the character is jerk who despises all his pokémon and travelling companions, constantly berates them and yet, they all either want to bang that character or they worship the ground that character walks on, then it's probably a Sue.