I went looking for something like that a while ago and kept hitting walls. Most 'neglected Naruto' fics just recycle the same plot: family ignores him, he finds a secret power (often a bloodline), comes back overpowered, and gets revenge. Adding magic usually means a crossover where he learns, like, Harry Potter spells, but the magic feels tacked on, just another tool for revenge. It rarely changes the core emotional neglect theme.
One exception I stumbled on was 'Of Leaves and Whirlpools' on FFN. Naruto is neglected by Minato and Kushina for his sister, but his escape is through ancient Uzumaki sealing lore, which the story treats as a form of ritual magic with costs and rules. It’s less about flashy fireballs and more about runes, sacrifices, and forgotten contracts. The magic system directly ties to his loneliness—he's communicating with sealing spirits, basically creating his own family. It’s unfinished, sadly, but the chapters that are there handle the blend better than most.
Otherwise, you might have better luck in crossovers with 'The Ancient Magus' Bride' or 'Magi: The Labyrinth of Magic', where the magic worlds are inherently mystical and could mesh with a neglected backstory, but I haven't seen a standout one executed well.