One thing to take note of when writing a story: No matter how dumb something may seem, someone will try doing it. So relying upon things like "No one ever thought to try that before" doesn't work very well (unless there is something to restrict how many people can try in the first place). Having abilities only be weak because of limitations the main character doesn't have, can work well. Having abilities be weak because no one tried leveling them before, doesn't work as well.
One of the most common methods of breaking a weak skill in fiction (shows up a lot in shounen) is the skill that has a high price to pay for it's power, but the main character has some way to mitigate that price (like regeneration letting them use skills that injure them).
Other ways to break weak skills is to have synergies people don't normally get access to. For example: if a person has a skill that lets them survive severe blood loss, it's not a big deal. Even if they can produce infinite blood, it's not very useful by itself (though there are still some weird uses). However, if they also have a skill that lets them use blood instead of mana to power spells (or obtain an artifact powered by blood), suddenly it's broken.
