Missing Abilities in my opinion:
Venusaur: Rock Smash
Charizard: Search
Blastoise: Rock Smash
Butterfree: Cut, Harvest, Search
Beedrill: Cut, Harvest, Rock Smash
Pidgeotto: Cut, Search
Pidgeot: Cut, Search
Rattata: Cut, Dig
Raticate: Cut, Rock Smash
Spearow: Cut, Search
Fearow: Cut, Search
Ekans: Sniff
Arbok: Sniff
Raichu: Dig
Sandslash: Minning
Nidorino/Nidorina: Cut
Nidoking/Nidoqueen: Cut, Minning
Clefable: Search, Light
Vulpix: Cut
Ninetales: Cut
Wigglytuff: Light
Zubat: Cut
Golbat: Cut, Search
Crobat: Cut, Search, Sniff
Oddish: Harvest
Gloom: Harvest
Paras: Harvest
Parasect: Rock Smash, Sniff
Venonat: Harvest, Search
Venomoth, Cut, Harvest, Search, Sniff
Diglett: Minning
Dugtrio: Minning
Meowth: Dig
Persian: Dig, Sniff
Psyduck: Cut
Golduck: Cut
Mankey: Cut
Primeape: Cut
Arcanine: Cut
Geodude: Minning
Rapidash: Rock Smash
Slowpoke: Light, Search
Slowbro: Light, Search, Teleport
Farfetch'd: Rock Smash, Harvest
Doduo: Dig, Cut
Dodrio: Cut, Rock Smash, Dig
Dewgong: Surf, Dive
sprite required
Drowzee: Blink, Search
Kingler: Surf, Dive
Exeggcute: Light, Search, Teleport
Exeggutor: Light, Teleport
Cubone: Dig, Find Hole, Minning
Marowak: Dig, Find Hole, Minning
Rhyhorn: Dig
Kangaskhan: Cut, Dig, Minning
Kingdra: Rock Smash
Seaking: Rock Smash
Staryu: Light, Cut
Starmie, Light, Cut, Search
Jynx: Light, Control Mind
sprite required
Magmar: Rock Smash
Pinsir: Rock Smash, Dig
Lapras: Search
Eevee: Cut, Dig
Vaporeon: Cut
Jolteon: Cut
Flareon: Cut
Espeon: Cut
Umbreon: Cut, Dig, Light, Dark Portal
Kabuto: Dig
Kabutops: Dig
Aerodactyl: Cut, Search
Snorlax: Cut
Dragonair: Cut
Typhlosion: Rock Smash
Feraligatr: Rock Smash
Sentret: Cut, Search
Furret: Cut, Search, Harvest, Rock Smash
Hoothoot: Cut, Search, Light
Noctowl: Cut, Search, Light, Harvest
Ledyba: Cut
Ledian: Cut, Rock Smash
Spinarak: Dig, Cut
Ariados: Dig, Harvest
Lanturn: Surf, Dive
sprite required
Togepi: Light, Search
Togetic: Light, Search, Blink
Xatu: Search
Azumarill: Dig
Sudowoodo: Cut, Harvest, Minning
Yanma: Harvest
Wobbuffet: Light
Pineco: Cut
Forretress: Cut
Gligar: Cut, Rock Smash, Harvest, Minning
Snubbull: Dig
Granbull: Dig
Shuckle: Rock Smash
Sneasel: Rock Smash, Dig, Harvest
Teddiursa: Dig
Ursaring: Dig, Harvest, Sniff
Piloswine: Minning
Skarmory: Rock Smash, Search
Houndour: Cut
Houndoom: Cut, Dark Portal
Donphan: Minning
Stantler: Dig
Miltank: Cut
Larvitar: Rock Smash
Tyranitar: Minning
Sceptile: Harvest, Dig
Swampert: Rock Smash