The other uses a Patrat.
I don't play League of Legends but I've heard some of the terminology and recognized an NPC in the Onyx Arcade at the game machines reference it, talking about "mid-laning" IIRC.
Most of the Silph Co.'s floors are closed off due to "security reasons in the Kanto region", referencing Team Rocket's attempted takeover of the company.
There's an NPC in the Onyx Arcade who says "Big money, no Krabbys" which is a reference to a game show called Whammy.
In Cain's songs are several references to the anime openings, the most recognizable being when he says "At this rate I'll never be the very best like no one ever was".
In a house in Calcenon City there's an NPC that says "I'm talking bout all-out party and we're getting it started. Mr. President, do you mind some electric guitar?". I looked it up because I thought "That's so bizarre it has to be referencing something" and it's a line from the theme song to Cory in the House.
The trainer in Charlotte's gym who says "See you in the Starlight Divide" is referencing Starlight Divide, the game Ame's making after Reborn is finished.
In Blake's apartment, after solving the puzzle Shelly says she feels like you should've been looking for a door with a number 9. This is a reference to a game, but I forget which one.
When Terra says that you won a brand new car, that's a reference to the game show The Price is Right.
There's an Arcade Star on Opal Bridge named Miku, a reference to the Vocaloid Hatsune Miku. Could also be a reference to a community member because I've heard there was someone named Miku here.
One of the Grand Hall trainers has shiny members of the Squirtle line and calls them Teenage Mutant Ninja Squirtles, a reference to Teenage Mutant Ninja Turtles.
Some NPC trainers are references to community members. There's Psychic Inuki (Inuki), Street Rat Erick (Neo), Street Rat Andreas (Eternal Edge), Arcade Star Lithi (not sure of her name, but she's no longer with us in the same sense as Corey and Kiki), probably some more I don't know about, and the PC programmer Nyu is also a reference to forum member Nyu.
Most of the characters themselves and many events in the game are references to the leaders and events from the online league, which the game is based on.