Niantic tries to add references to the Anime in Pokémon Go. The following is a list of Easter Eggs that have been discovered.
The most well-known Easter Egg is the Eeveelution Easter Egg. In the anime episode "The Battling Eevee Brothers", there are four brothers each with a different Eeveelution. Mikey, the youngest has the base form, Eevee, who is pressured by his brothers to evolve Eevee to one of the different forms. Sparky has Jolteon, Rainer has Vaporeon, and Pyro has Flareon. In Pokémon Go, the trainer can nickname their Eevee with the three older brothers' name to get the corresponding Eeveelution. This Easter Egg was confirmed by Niantic CEO John Hanke at the 2016 San Diego Comic Con. However, it can only be done once for each eeveelution.
This naming trick has been been extended to include the Gen II Eeveelutions. In the animates series, there are five sisters called the Kimono Girls who each have a different Eeveelution — the most notable being Tamao's Umbreon and Sakura's Espeon.
Starter Pikachu Edit
The other most well-known Easter Egg is the possibility of getting a Pikachu as a starter, just like Ash. At the start of your journey, Professor Willow will give you an introduction to the game and Pokémon, then you will be given the task to capture a Starter. The three starters from Kanto appears, Bulbasaur, Charmander, and Squirtle. If the trainer wants Pikachu, then he/she has to walk away from these three 4 times. (They will disappear and respawn in front of you so don't worry). On the fifth time, the trio will be accompanied by a Pikachu.
Pester Ball Edit
Pester Ball is a lesser known Poké Ball that made its appearance only within Pokémon Snap. In the game, the Poké Ball has the same effect as Repel which helps the photographer take photos of Pokémon. It is also special because it has four different colours, Red, Orange, Blue, and Purple. The center of the Poké Ball is purple, then, going clockwise, the outer layer is divided into three equal parts of Orange, Red, and Blue. This Easter Egg will appear in the app by holding down the Poké Ball icon and then sliding your finger to each of the four icons of the menus, without lifting your finger. A coloured ring will temporary appear showing Orange for Pokémon, Red for Pokédex, Blue for Items, and Purple for Shop.
In the first Pokémon games, Red and Blue, the trainer can finding a glitch in the game called Missingno. This Pokémon appears as pixelated blur and tends to cause problems to the save files. In Pokémon Go, Niantic implemented the Missingno. Easter Egg in the Egg section (only accessible for iPhone). If a trainer goes to the Egg section, click on an egg and then double-click the home button on your phone, you can see the arrangement of numbers and letters, possibly a reference to Missingno.
Also in the Egg section, there are trainers who have encountered a weird quote saying "Hatch this egg by feeding it butter. It likes all kinds of butter, every kind. The best kind." This could be a reference to Alice in Wonderland or it could imply an item that is yet to be introduced that helps with Egg Hatching.
Pokémon Animation & Sound Edit
If a Pokémon is tapped while looking at the Pokémon list, it will perform its battle animation, and its cry will also be heard. Pikachu is the only Pokémon that will say its name; just as it does in the anime series.
Pikachu on Shoulder Edit
Initially when a Pikachu is assigned as a buddy, it will show up on the ground beside the trainer. However, if 10 or more Pikachu candies are collected, the Pikachu will appear on top of the trainer's shoulder. This is most likely a reference to Ash's Pikachu always being on his shoulder.