When my brother and I typically debate things we usually come to the same agreement. However, this time we've come to a very different conclusion. What we were debating was whether or not it is actually possible to have a Mary Sue within the actual Stargate Universe as Stargate uses string theory within canon.
My brother stance is that any character that is from within Universe that would under normal circumstances be labeled a Mary Sue or Gary Stu would in fact not be a Mary Sue because the existence of said character can be explained if one uses string theory, as you can come up with an actual explanation as to why the characters are able to exist and thus be believable. If you add in an actual alternate universe though, you come into a completly different matter as string theory can not be applied.
My stance is that string theory can be applied to any fandom that exists in order to create an AU that falls under the sub category of Alternate Reality. However, it is up to the writer and not the reader to make it apparent that string theory is being used from the very beginning and not leave it up to the reader to suspend their disbelief or come up with the logic needed to believe that the story can really happen. For example, if the laws of physics do not apply in one of the alternate realities then the writer must in fact make it clear at the very begining of the fanfic in some manner. A writer also can not come out later after their story has been labeled as problematic and use string theory to explain things unless the writer is capable of crafting a believable string theory explanation, which is slim if the writer did not put thought into their story from the start.
In other words string theory is more complex then simply saying that anything can go. The impossible must be made possible by the writer.