Honestly considering this is "horrible fanfiction ideas", I can write whatever I want here. I am not sure if these have been done before tho.
Mixed Blessing System.
So, here is the catch. The Protagonist is allowed to choose X amount of powers (fully dependant on how much the author is willing to put it). These may give you powers, but also curse you. For an example I'll take an example of a roguelike called "Shotgun King". In this game you have black cards and white cards. Black cards benefit the player, but might also reduce your aim, speed, firepower, blade, etc. The white cards mainly benefit the opponents, but might also benefit the player (reduced speed, hp, etc.). Now, you might be asking: "Why don't I only choose black cards to be OP then?" Well, each black card links up with a white card. And if you choose a black card, you also have to deal with the consequences of the white card. There are certain combos that you can do with black and white cards. For an example: In a modded version, there is a black card that completely makes a type of enemy able to attack you, unless you kill one of that type. This makes all the white cards that affects that type of enemy useless against you. This isn't practical in a novel setting considering you wouldn't want someone to fight against one type of monster all the time, but it's just an example.
True Gamer System.
So, everyone on this site probably knows the gamer system. Leveling up your stats by doing missions IRL, something like that. Well, what if you just complete missions in a game? (Or it puts you in the game so that you beat it [has been done once from what I've seen])Or what if the system rewards you by making you able to transform into a character of the game you just finished? Maybe transferring all of the stats to your actual body, giving you skills from the game, the list goes on. What I'm saying is that people with the gamer skills are way too limited in their imagination. ID create? Fighting zombies? Daily workout? These honestly are cool, but seeing them in most gamer fics I read is honestly getting bland.
Off-topic
Try the game Shotgun King, it's pretty fun with mods. (It's a roguelike tho. Some people really don't like them) Also school started again this week so I might not post much. I realized I wrote too much about shotgun king now that I saw the word count.