depends on the type of Ability. So yeah by default i'd all group them under Ability and then branch out into specific Types. Kinda how Heroes (the TV Series) did it combined with the general D&D Idea of it.
Elemental, Mental or Mutation for one, to define how the Ability works, i.e. its basic Type. Everything that refers to a elemental force for attacking/defending is grouped up under Elemental, so Fire, Water the whole thing.
Mental would be everything which is done with the Mind, Teleportation, Telekinesis, Telepathy, Sensory Manipulation and so forth would be grouped under that.
Mutation basicly is everything which is based on the Body, Super Strength, Super Speed and so forth go under that one.
So its all about how you group them up, but i refer to them collectively as a Ability rather than Magic, since even Magic is limited and not entirely encompasing the whole field of things one might be capable of. As for the most part Magic tends to refer specifically to "magical" Abilities such as generating Fire or Ice or something like that yet doesnt include other abilities like Telepathy and so forth or Powers which are purely physical, like Speed and such.