These are probably the things the API will have to be adjusted for:
* Debuff display on players (Target structure change, probably packet change or a new packet)
* Focus Target (New target structure, adding to get_mob_by_target, adding new structure and phrase to shortcuts/gearswap)
* Increased merit caps
* Increased Job Point caps
* Targeting GEO spells (possibly just GearSwap/Shortcuts changes)
* New area (POLUtils, ResourceExtractor, FFXIDB plugin/website)
* New magic (unknown potential changes, or not)
* Potential action packet adjustment (to use those empty 12 bytes added last patch - Probably tied to GEO spell positioning)
* New icons for SP2 abilities (Blazing Rush, etc.)
* Armor and Weapon .DAT format adjustment?
Of all of these, I feel the Geomancer spell changes have the highest potential for annoyance based on the vague way they described them.