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Expand what skills cover to general areas. The reason I say this is related to Supers games I've been doing. Rather than having separate skills for knowledge: physics and knowledge: chemistry for science types (like Iron Man); and Knowledge: arcana and spellcraft (say), or Dungeoneering, the planes, religion, etc., I decided to have the heroes base their skills of Power Sources.
A knowledge skill is used primarily for exposition: the DM tells the PCs what their characters need to know for that encounter and/or adventure. So having obscure areas of knowledge that have no real game effect and take up points, is not fun: skill ranks are used up, and no reliable exposition happens.
Ergo: let general areas of knowledge be based around power sources or important areas. So Knowledge: Metaphysics covers Arcana, the planes, undead, aberrations, etc. There would be different DCs for what the PCs are familiar with ("as a wizard, this knowledge is slightly more obscure for you than for our Cleric"), and there could be specialization feats for arcane info, creature types, religion, etc. Otherwise, everyone could have a "knowledge" skill, or a broader type.
Knowledge: metaphysics (the planes, arcana, religion, dungeoneering, what a staff of the magic does, the effects of power word: blind)
Knowledge: History or martial (nobles, heraldry, local, recent wars, geography, etc.)
Knowledge: Bestiary (dragons, beholders, undead, what type of wood to use to slay an elven vampire, etc.)