I'd definitely look over weaknesses/resistances, and some pokémon typings. It's hard to say any of these would be a given since it might shift the balance too much but:
Water weak to ice.
Steel weak to electric but resists fighting.
Electric weak to dragon.
Flying no longer weak to ice, and no longer resists grass.
Fighting no longer weak to flying, hits neutral against bug.
Rock no longer weak to grass.
Ground no longer weak to water, but weak to bug.
Ice resists water and normal, but is resisted by rock.
Normal resists bug.
Bug no longer resisted by fairy, fire or ghost.
Pokemon type changes (With moveset additions where relevant):
Swablu, Starly line, Farfetch'd: Nor pure flying type.
Gyarados, Goodra line, Now Dragon/Water (Double weak to ice).
Ekans line: Now normal/poison
Ninetales: Now Fire/Ghost
Shellder line, Clamperl: Now Water/Steel
Huntail: Now Water/Dark
Gorebyss: Now Water/Psychic
Bellossom, Comfey: now Grass/Fairy
Sunflora/Sunshine Cherrim: Now Grass/Fire
Golduck: now Water/Psychic
Starmie, Slowpoke, Slowbro: Now pure Water.
Politoed, Azurill: now Water/Normal.
Porygon Z: Now Normal/Ghost
Shinx line: Now Dark/Electric
Manaphy: Now Water/Fairy
Rockruff/Lycanrock day: Now Normal/Rock
Lycanrock Midnight: Now Dark/Rock
Komala: Now Normal/Grass
I'm sure at least some of these could be changed without messing up the balance completely.
Maybe Doopliss isn't kicking ass, but he's taking names!