I would consider a 100% run to be

Main story completed (obviously)

All side quests finished

Complete maxed out Pokédex (not just level 10 but all research tasks complete and perfect) (and Darkrai and Shaymin are not required)

All clothes and accessories unlocked and owned

All items and crafting recipes unlocked

Max rank

All wisps

All alpha Pokémon caught

All Unown

No Trading for Pokémon they must all be caught