Well, yeah, I guess. I think changing the basic rules of the setting but having characters that are recognisably the original characters (e.g. an AU placing the original characters in different universe with different rules) is OK, although I think it probably only works if it doesn't try to take itself too seriously, as is a completely OC-filled story set in the Nasuverse, but changing both makes it no longer a fanfic in any meaningful sense, and if you're going to do that you might as well just call it an original work (certainly I've had ideas before where the characters are based on Nasuverse characters, but are different enough that it would be meaningless to call it a fanfic). I think there is some leeway there, though, particularly in the case of porn (and especially porn with images), since in that case what the character looks like does matter somewhat.
As for the "Shirou is a Gary Stu" thing, that's more just bad characterisation and bad writing, really. I don't think disliking bad writing is exclusive to you, I think everyone does (although they may not always agree on what constitutes "bad writing"). I'd say there's a definite distinction between someone just not writing a good story and someone writing a good story that is a fanfic in name only.