If the game is meant to be a sort of "New End game" or "Super powerful end game items early on" I have no problem with it. If that is what it is for there is no issue.
Heck your example of the BFS-9000 mod? No issue whatsoever.
I mean more what I always call "Special snowflake syndrome" with mods. If a mod adds in something it MUST be better, more special, and more amazing then anything currently in the game no matter what it is.
So if a Skyrim mod added, for example, enhanced martial arts system with its own tree, weapon types, and stuff.. basically to make it viable. 9 times out of 10... It will either be
1) Far too ridiculous to use
or
2) Far better than everything else that breaks the game's curve in two, shattering the game into pieces.
Heck if the mod was for allowing you to use books as blunt weapons... those books will be more deadly then swords.
It has nothing to do with "Being fair", but more to do with the fact that to me... a good mod takes the base game into account. Assuming it isn't trying to break the base game intentionally.
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Basically it is why I like The Long War 2... It actually tries to take gameplay into account, its modifications are based around the meta and gameplay.
As opposed to "Screw the gameplay!" mentality.
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Mind you this all excludes other types of Mods... which I kind of wish the Steam Workship would separate "Quality of life" mods, "UI" mods, and "Content" mods... I've used quality of life and UI mods and sometimes they are essential... But they are very popular and sometimes MORE popular then content mods. I'd love to wade through mod content.
Rimworld is the only game I currently heavily mod... But I've culled a lot of mods.