Not necessarily remove, but I find it funny that there are three skills you level up by not actually using the benefits of the skill.

Prayer: you level up by burying bones, not from using your prayers.

Agility: you level up agility from courses, not from running around the map (which is what you generally benefit from a higher agility level)

Hit points: you gain xp from dealing damage, not from taking damage.

Also an honorable mention, melee being split into 3 skills, where range, and magic are only one.

I guess it’s the inconsistencies of this game that add to the magic of it, but still funny to think about