The pokemon equivalent of those neglected Naruto fanfics is betrayed Ash fics as they're both edgy for the sake of edgyness.
To make a Naruto neglected fic just take a look at Boruto have both his parents simply be overworked and barely have enough time for him rather than just hating him for no reason.
These fics usually have siblings as well so have Minato and Kushida simply be spread thin between their triplets and sorta just neglect Naruto not out of malice but because he seems the most self sufficient, like what happens in real life where parents ignore the most self sufficient child.
You can have a "betrayed" Ash fic where his friends want him to quit not because they don't believe in Ash's dream, but because Ash has died various times, is targeted by team rocket, and is constantly finding himself in dangerous situations.
They want Ash to quit because they fear for his safety not anything to do with just hating on him randomly which is way more realistic.