The completion rate displayed by the game after one beats Ganon is actually a map completion percentage. It only counts things that appear on the map: divine beasts, shrines, korok seeds, and named locations (like bridges, etc.). But there is a lot more to do in BotW: side quests, mini-games, memories, gear, sub-bosses, the compendium…
To keep spoilers to a minimum, I list numbers but as few names as possible. Keep in mind that some items may require amiibo, so for most of us full 100% completion may not be attainable.
I've spent a lot of time researching this list. I hope you will appreciate it and find it an useful resource. Please help me fix any omissions and inaccuracies. Thank you.
Mandatory: . Destroy Ganon . 4 Runes . 1 Paraglider "Optional": . 4 Divine Beasts . 15 Towers . 120 Shrines (42 Shrine Quests) . 2 Ancient Tech Labs . 4 Great Fairy Fountains . 900 Korok Seeds . 18 Memories (12+1 Captured Memories) . 76 Side Quests . 16 Mini-Games 8 Ability Controls Inventory: . 127 Weapons . Master (Hero's) Sword . 26 Bows . 8 Arrows . 33 Shields . Hylian Shield . 81 Armor (21 Armor Sets) . 150 Materials . 62 Food . 123 Cooked Food . 11 Elixirs . Horses: . Epona . Giant Horse . Horse Fairy . 6 Bridles . 6 Saddles Upgrades: . Sheikah Slate . Sheikah Sensor . Bomb Rune . Stasis Rune . 67 Armor (to level 4) . Inventory: . +11 Weapons (to 19) . +8 Bows (to 13) . +16 Shields (to 20) 223(?) Named Locations: . 9 Villages . 15 Stables . 7 Landmarks Medal of Honor: (unique locations, respawns do not count) . 40 Talus . 40 Hinox . 4 Molduga 23 Lynels: . 7 Red . 8 Blue . 8 White . Except for the ones at Hyrule Castle and Ploymus mountain, all Lynels rank up to Silver as the game progresses Coliseum Ruins 3 Dragons Lord of the Mountain 385 Compendium: . 83 Creatures . 78 Monsters . 36 Materials . 184 Equipment . 4 Treasure Enemy evolution: red < blue < black < white < silver
Source: official guide, internet, reddit comments