Systems are supposed to be another power system, but one that's based on gsmes and thus familiar to a lot of us nerds. Their biggest pro is that it gives the main character an immediate reward for their hard work. But a very common problem is when authors don't include the hard work. When that happens, it's just the main character getting a bunch of free power undeservingly, and leads to really bad and lazy writing.
Fanfiction has a stigma attached to it for bad writing. It's not always the case, especially with the ones I read (eg. i will touch the skies), but when I see a system where it doesn't belong to whatever story the fic is on, it's an immediate red flag that the author has no clue or desire for proper character growth or power progression. The original world likely has its own power systems, scaling, and progression, and a way for a clever author to insert their own character into it, to be a oart of the existing world. To throw it all out for something else that requires little thought shows that the fanfic author doesn't know, care, or is too incompetent to actually work with the world.
Like a Naruto fic. Why the FUCK would you have a system when the entire main point of the original story is a out the importance of hard work and perseverance? A fanfic main character has better work for their power like the others in the story. And if a hunter x hunter fix went with a system instead of something as complex, balanced, flexible, and creative as Nen? Then that fanfic author should be writing something else because they obviously don't appreciate the original story and likely just want to imagine their self insert getting with the chick with the vacuum.