I agree with @TrashyHuman . The way you put it, your system is deux ex machina, giving rewards without effort. And if it's doing that for MC, it should be doing it for everyone else too... which I imagine would get tricky to handle soon. If the system has to stay, the MC should be working hard for the special abilities he gets, pushing the limits of the basic class I assume he got, or trying to work outside its usual boundaries.So it's Kumo desu-ga and Tensura-type. Skill tree and class evolution stuff, you know
For example:
In this story, my MC is orientated to be a fighter, but he doesn't have the physique of a fighter. So the System gives him the ability to find his opponent's weakest point. It's not as simple as it sounds because even if the MC decides to attack that point, the percentage of success is never 100%. Therefore, after going through several battles and winning, Sytem gave him a skill that could increase the success percentage of his attacks.
Sorry if this sounds too complicated, English isn't my first languange
I like Sytem stories and think they're fun, like Solo Levelling and Tensura. Even though story-wise it's standard, it's something interesting to follow. But, the problem is that I don't know what makes it so interesting
Also, get rid of the "hard-coded" success chance. Make it dependent on the MC's execution of the skill, the accuracy with which he can hit the weakpoints. As he works on it, give him a boost to his agility/speed, that would translate in more accurate execution of the skill.