Allow: Anything that someone wants and comes up with a reasonable excuse for taking.
Use: Whatever fits the current setting.
For a more general structure? Well, for a quick generic system (I tend to make one tailored to a given setting) most things fit into one of the following catagories. Some sample subspecialities are included in ().
Supernatural Forces (Divided into Magic, Psychic, and whatever we’d call the Alignment Forces)
Arcane Lore (Runes, Glyphs, Spells, Spell Research, Potions, Power Ingredients, Ancient Enchantments,
Psychic Lore (Psionics, Soulmelds, Psychic Devices, Mentatics)
Religious Lore (Spirits, Gods, Theology, Death, the Outer Planes and their Creatures)
Living Creatures (Divided into Structure, Activity, and Development)
Behavior (Psychology, Criminology, Modeling, Insanities, Animal Training)
Life Sciences (Biology, Botany, Naturalist, Herbalist, Medicine, etc)
History (Archeology, Civic Development, Current Events, Nobility and Royalty, Paleontology, Evolutionary Theory, Creation Accounts, Developmental Theory, Ecology)
Natural Forces (Divided into Theory, Application, and Aberrations)
Physics (Optics, Astrophysics, Radiation Physics, Field Theory, Exotic Matter, Etc)
Engineering (Electronics, Clockwork, Mechanics, Armor, Weapons, Metallurgy)
Planes (Inner planes, Alternate Dimensions, Gates, Summoning Effects, M-Theory)
The Physical World (Divided into too small to see, big enough to see but small enough to manipulate, and too big to manipulate readily)
Earth Sciences (Geology/Geography, Hydrology, Meteorology, Navigation, Nature, Astronomy, caverns).
Constructs (Architecture, Mining, Statics, Construction, Dredging, Artifacts, History of Building Techniques, Crystallography, Local Knowledge (physical layout)).
Chemistry/Alchemy (Toxicology, Explosives, Plastics, Synthesis, Biochemistry).
Information Sciences (Divided into transmission, accumulation, and abstract interaction)
Communications (Linguistics, Ancient Languages, Art, Philosophy, Propaganda, Printing).
Culture (Sociology, Law, Business, Civics, Government, Streetwise, Politics, Local Knowledge/Culture).
Abstract (Mathematics, Games Theory, Tactics, Formal Logic, Information Theory, Cryptography).
Now, I'd tend to expect people to take general skills and specialities building on them - spending a skill point or two in exchange for a fairly large bonus on things like Culture/The Odantin Nomads. It might be worth finishing up a general structure at some point, even if it does have less world-specific flavor.