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To further compound this, the Diamond & Pearl episode "Where No Togepi Has Gone Before!" has a female Togepi's Attract working on Pikachu, meaning it's male, if Attract works the same way in the anime as it does in the games; in the actual games, the "Satoshi's Pikachu" event Pikachu that represents Ash's Pikachu is guaranteed to be generated as Male.
One could also argue that Giovanni is the center of a Love Triangle with Meowth and Persian. Meowth's Boss fantasies sometimes make Giovanni go Chibi and other times make him very Musclebound. But typically Meowth's ultimate goal seems to be just being petted by Giovanni.
Then there's Ash and Gary once it stops being Foe Yay.
Morty spends nearly all of For Ho-Oh the Bells Toll withdrawn and sullen. Bear in mind that in previous episodes he was outgoing and happy. The target of his attitude switch is his friend Eusine, who's shown up with a Suicune fixation and a bad temper, leading many in the fandom to believe that the two have an unresolved past relationship. Also bear in mind that Eusine's subsequent Legend of Thunder appearance has him in turn being upbeat and caring, so it may be a two-way street.
Brock and Ash have their fair share as well. Particularly in the episode "Two Degrees of Separation" where in one instance Brock introduces Ash to a female driver named Claudina who he'd been hoping to score with. Interesting to note that in the entire time he's doing so he's being all touchy feely with Ash, hugging him close and poking and prodding at his face in a playful manner. Later, he finds out that Claudina already has a boyfriend and she drives away. Which leads to this scene from the English dubbed version.
In the episode Love at First Flight May tricked Ash into dressing up as a woman they had just met, named Juliet, in order to help a man named Romeo confess the feelings that he had for Juliet. Brock tried to help out too and ended up getting carried away, even chasing poor Ash around and trying to hug him while declaring "My sweet Juliet! Heal me with your love!" * releases hearts*
Pokemon Special has its fair share of Ho Yay moments. In the FRLG arc, fans have taken to pointing out that Green is Red's coathanger. Gold and Silver had some rich Foe Yay vibes in the GSC arc when they first met, and by the end of the arc has Silver tearing up a little when he thought that Gold was lost in the timestream. It culminates to the point that Gold blushes when Silver reveals that he was conscious when Gold called him his friend in the Emerald arc. Dia and Pearl need no explanation, and their brief falling out in the middle of the arc can almost be taken to be a breakup.
Satoshi and Shigeru in Pokémon Zensho have the same Foe Yay as Red and Blue in the games. To top it off, at the end they have a sincere moment and end up becoming friends again.
Red and Blue. Blue's description of having been your friend gone rival makes him sound Tsundere toward Red, you have Foe Yay for most of the original games, and once you go back to being friends he seems to think about him a lot.
In the original Red/Green/Blue/Yellow versions, the Lass trainers comments to the player also are either flirting with you or accusing you of being creepy towards her. In Leaf Green these are unchanged if you play as Leaf.
The ferris wheel dates in Pokémon Black and White are full of Does This Remind You of Anything? in the Japanese version. Two of the characters you can date are of the same gender as the protagonist - Waitress Aurora for the female protagonist and Hiker Andy for the male. Andy comes off as a Hard Gay who constantly talks about the heat and asks you if you've ever had a lover (in context it sounds like he's seducing you). Aurora sounds like she's coming onto you, though the Japanese version has her talking about a boy. In the English version the Les Yay was upped due to lack of reference to the boy and in the French they made the boy into a Pokemon of hers.
Not to mention everyone taking N and Hilbert's ferris wheel scene as Ho Yay as well.
Expected, since N has a lot of romantic subtext with the protagonist regardless of gender, it only gets more overt in the sequel, with N saying lines like "There is also a Trainer I want to tell how I feel..." obviously referring to the protagonist of Black and White.
The female protagonist in Black 2 and White 2 can get a ferris wheel date with a rocker girl, who would sing a surprisingly romantic song to her while on the ride. She'll also say that she can only show her true image around you, and will sing more for you next time she meets you.
Hiker Andy returns as a Ferris Wheel encounter for the female playable in Black 2 and White 2... but all he wants to talk about is his great romance from two years prior (the previous games).
In Black 2 and White 2, when they visit Join Avenue, Elesa keeps up the trend of looking for stores run by dazzling cute girls while Marlon asks for stores run by very energetic men.
Speaking of Elesa, there's her rather popular shipping with fellow gym leader Skyla. They are canonically close friends...
In X and Y, if you play as Serena instead of Calem, Shauna's very visible attraction to the player character remains. This can get delightfully yuri-ish during such wonderful moments like the emotionally-charged fireworks cutscene at the palace.
There is a Brains-and-Brawns Double Battle formation with a male Martial Artist and a male Psychic trainer (Trainer names Frank and Sly) in Kalos. When you win, the Martial Artist will cry and the Psychic will try to comfort him in a surprisingly tender fashion.
Lumiose City's (female) hairdresser will get rather... distracted... by the cute looks of your female player character once you raise your hidden Style rating enough and become a 'regular' customer. She'll also start making more small talk with you while asking you how you want your hair done, and one of things she can do is compliment you on your choice of fashion.
During X and Y, if the player goes to the Transportation Services building in Lumiose City, they can go to the second floor and talk to the NPCs who work there. One of them, a blond man, will be startled and proclaim that you shouldn't sneak up on him like that and that his heart is beating so fast because of you. If you talk to him again he'll claim he's not in love with you. He'll say this to the male player character as well as the female one.
Professor Sycamore is so enamored by Lysandre's "passion" when he angrily explains to the player how unjust the world is, the idea Lysandre alludes that genocide was a viable option to deal with it seemed to fly straight over Sycamore's head. The fact they're said to have had a friendly past together does not help quell the shipping that ensued.
Sr. and Jr. Anna & Meg from the third generation. If they call you in Emerald, you'll speak to Anna, who says that both Meg and Pokémon are "so cute!". The two will then have an argument during the call, where Meg complains about being Anna's slave, and then Anna gives you this lovely quote:
Anna: "I wouldn't treat you like a slave, Meg! You're too special to me!"
The same couple in Omega Ruby/Alpha Sapphire (now called Teammates) have much more romantically suggestive dialogue about one another when you first encounter them.
A pair of NPCs appearing to be of the same Trainer Class shows up on Sea Mauville in the remakes inside a room that requires a key to enter. When talked to, the senior demands to know how the player character got in, as she was certain she locked the door, while the junior just blushes.
You can literally invoke this to most of your Genderless Pokemon! If you bring one (like a Metang) to a Daycare Center together with a Ditto (another genderless Pokemon), you will eventually receive an egg containing a non-Ditto baby (for this case, Beldum).
You can also invoke this in Pokemon-amie with the corresponding gender.
Lisia from Omega Ruby and Alpha Sapphire can definitely come off like this when the character is female; constantly spurning Chaz's advances, blushing around the player character, and seeming to very interested in their Coordinator career. Not only that, when the player first beats the Hyper Rank contest, she nervously suggests the player and she do 'something' that she can't elaborate on due to Chaz being a Moment Killer.
Wally is this in spades in the remake, if you play as Brendan. Gaining an actual personality from the remakes may have helped, but the fact that Wally is super moe, constantly blushes and around you and is more nervous than Hinata confronted with Naruto gives off strong waves of a crush. It doesn't help much that his proposition to be your rival sounds a lot like a love confession.