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 Shipping. The image source comes from a scene where Gary is seriously injured in the Viridian gym.
Morty spends nearly all of For Ho-Oh the Bells Toll withdrawn and sullen.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.
There's also a bit of this between Pikachu and Meowth, doubling as Foe Yay Shipping:
One of the Japanese endings (which was sung by Meowth's seiyuu) even featured the two dancing together. note A rather humorous bit of trivia regarding this pairing—Meowth and Pikachu are part of the same egg group, meaning that if one of them was female, they'd be capable of breeding!
One Johto episode revolves around the two being stuck to one another and away from their humans. After they ease up around each other, they share a scene where they eat an apple together.
This scene, where Seymour hugs Ash for saving him.
Misty's excitement over meeting her water Pokémon idol, Prima, seems at times to be rather focused on Prima's chest.
The introduction of gender differences in some Pokémon into the anime's canon has actually unintentionally retconned Ash's Butterfree into possibly being homosexual in the episode "Bye Bye Butterfree". Ash's Butterfree ends up finding another Butterfree as a mate, and neither of them have the characteristic spots on the lower parts of their wings◊ that female Butterfree have. Making the other Butterfree pink was likely meant to imply its gender, but the existence of Pokémon with exotic colors in the anime (including Butterfree itself), coupled with the established idea that people have assumed a Pokémon's sex before only to be wrong, means that the possibility of Ash's Butterfree mating with another male is still there. This was most likely due to the fact that this episode was written before the mechanics of Pokémon gender differences and shiny Pokémon were even thought of and introduced. Pokémon: I Choose You! recreates the events of this episode and properly depicts the pink Butterfree with wing spots.
Advanced Generation
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*
Dawn and Zoey contrast one another: one is blue-haired and dresses in princess-like Coordinator apparel and the other is red-haired and dresses in prince-like Coordinator apparel.
Dawn becomes friends with Zoey quickly. Zoey offers to help Dawn with her hair when they're still strangers.
Dawn blushes after Zoey compliments her and wishes her luck on her first contest. It could be blushing from being nervous about the contest, or it could be blushing because of Zoey.
It doesn't help how hard Dawn took Zoey's words to heart.
During a festival in Sinnoh, Brock gets a lovey dovey over what appears to be a shady male guy and flirts with that guy. However, this shady guy actually turns out to be Officer Jenny in disguise, meaning that Brock saw through her cover.
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.
There may be something between Ash's Pikachu and Dawn's Piplup? (Granted that ending includes the other Pokémon too but still). If not, they're at least Heterosexual Life-Partners or Those Two Guys.
Best Wishes
Ash and Cilan get this with Cilan's very campy nature and Hero Worship of Ash, which often comes off as obsessive or romantic.
When N showed up in Best Wishes, fandom speculated there'd be some of this between N and Ash. (Never mind N is a lot older and Ash is 10.)... seems like◊ the shippers◊ were right◊.
The B&W episode All For The Love of Meloetta brought back Cynthia. When Ash talks to her, he and Cilan act as they usually do while Iris stares vacantly at her. When Cynthia does try to talk to her, Iris outright blushes and twiddles her fingers as if she were talking to someone she had a major crush on. Cynthia's outfit doesn't help considering how much more relaxed it is compared to her Sinnoh outfit. Turns out she just wanted to battle the fellow dragon trainer and was too nervous to ask, but still...
X and Y
Alain from the Mega Evolution specials had no real motive to enter the Kalos League and was not collecting badges until he met Ash and his particularly special Greninja. Come 2 episodes before the big event, and Alain has alreadycollected enough badges to enter the league. His motive to do so? Just to fight Ash. Weirder still is how Alain has the special benefit of just walking to a trainer and ask for a battle, but he makes the occasion very important just for Ash. The fact that he even comments that he never felt this strange feeling until fighting Ash, and he was seen smiling from this. Mind you, he has been scowling ever since Act 4, and it was fighting Ash that brought him smile.
Clemont has been thoroughly inspired by Ash, always looking up to him. Ash meanwhile is ever impressed by Clemont, and is even fascinated by his inventions. Ash never showed negativity towards his leanings on science (something even Bonnie showed frustration). And there's that angst he had, thinking he "couldn't satisfy" Ash in battle which leads to him leaving the gang for a while. The gym battle itself is Clemont dedicating himself towards Ash. And then there's the insert song "Kira Kira", which is referred to as Clemont's character song, a song about him being inspired by Ash and saying how much Ash means to him.
Sawyer adores Ash and sees him as a role model, but the defining moment was definitely him repeating Serena's words of "Welcome back, the one I admire" during their final battle, when he realizes that Ash no longer is down after loss to Wulfric. Considering that context of the situation is the same as Serena's and Serena's status as Love Interest means that he definitely saw Ash as more than friends or rivals.
Professor Sycamore manages to sniff out Meyer's secret identity as Blaziken Mask by... inhaling the scent of a dirty oil-stained rag (and commenting on 'the fragrant flavor of oil' in the process) that Meyer had asked for, and later identifying the same scent on the Keystone Blaziken Mask lends him. When Sycamore next approaches him, he does so while commenting on how he never gets sick of the smell in a very sing-song, flirtatious voice, leaning into his personal space, and saying he wants something else from Meyer than just repairs.
Sun and Moon
Mallow is very protective of Lillie in the anime, always encouraging her to get over her fear of Pokémon and even dragging Ash into spying on her at one point. A promotional image for a plot involving the Ultra Beasts even has them holding hands while surrounded by Xurkitree and Blacephalon.
In Sun and Moon Episode 93, Mallow and Lillie do a full blown Revolutionary Girl Utenareference◊, which added even more fire to their ship.
In Pokémon SM058, an alternate color Toxapex (colored to resemble James when poisoned by his Mareanie) tried to give James a Corsola Horn. Which is popular among female Mareanie (and presumably among female Toxapex as well). After both fought over James's—female—Mareanie and James saved both the alternate color Toxapex and Mareanie from a Tentacruel who lunged at them. The alternate color Toxapex is male. James is male. James's Mareanie—who is also smitten with James—caught on, chasing after the alternate color Toxapex as he was chasing after James with him smiling and blushing all the way. Instead of trying to help her teammate, Jessie watched as both Pokémon hobbled after James and called him a stud. A stud among Mareanie and Toxapex, female and male.
It isn't just Lillie that Mallow seems to be shipped with, as she's also shipped with Lana, as episode 59 revealed that they've been Childhood Friends, even holding hands a few times as small kids! Also, during Kukui's wedding, they were seen celebrating pretty close together, and there's even subtext between the both of them in the manga version as well.
When Ash and Goh meet for the first time, Goh immediately calls Ash his friend. Delia specifically asks Goh to look after her son (to which he replies he will with sparkles) and they also share a room together.
In JN003 Goh is blushing at Ash after being embarrassed for how they fought earlier on asking if they can be friends, to which Ash states they already are friends. It wasn't even the first time in that episode; Goh was frequently blushing towards Ash in either bashfulness or awe throughout the runtime as they interacted with one another.
Scorbunny teases Goh about his admiration of Ash, causing Goh to suddenly start acting Tsundere and blush like a schoolgirl.
Goh is embarrassed he is holding Ash's hand in JN058.
On Ash's side of things, we have the time he was possessed by a Shellder and started acting weird(er than usual), calling Goh "my dear Goh" and wanting him to rule by his side.
In JN058 Ash casually holds Goh's hand while reassuring him with his words, plus when Goh asks if they need to hold hands he hesitates before making an excuse he and Goh need to hold hands using since Goh can't see.
He also pushed Goh in the bush earlier placing his hands on Goh's back and usually likes to get physical with Goh in a way he doesn't do with others.
There have been many fanfics about the point Ash and Goh share a room which could lead to situations and they take care of all the Pokémon together like parents.
In JN135, the way how Goh is offended with Ash being so casual about travelling without him can be interpreted like a couple not seeing a problem with being apart. His words were also "We're through", something more commonly associated with breakups.
Character of the Day Hodge from Episode 7 calls Goh cute, which he takes offense with. In most versions he then tries to disguise it claiming he meant his behavior was cute... except for the French dub, where Hodge doubles down on it instead by saying "I do think you're cute with that Taillow on your shoulder!"
Goh and Horace, his Childhood Friend, in JN032. From the moment the preview of that episode was shown, people were already interpreting Horace as Goh's New Old Flame, given the way he acted like he was Stood Up by him. The episode ends with Goh and Horace rekindling their friendship and walking slowly towards each other while staring at each others' eyes fondly, but the camera pans up to the sky as if to leave it ambiguous whether they hugged or kissed. View here and judge for yourself.
Not helped by the way the narrator describes how Pokémon create many kinds of bonds in ambiguous terms, as well as how two Celebi (one pink) are seen watching the pair, clearly meant to be representative of Goh and Horace, as they are reunited with one another...
Chloe has quite a few Les Yay moments with the girls she has befriended.
In JN074 and JN075, Chloe meets and befriends Dawn. After the two confront a sleep deprived Rhydon and knock it out in battle, the two praise each other and end up holding hands, while the two blush at each other. Later, while they're camping out at night, Dawn decides to introduce Chloe to the idea of Contests, and grabs Chloe and holds both of her hands.
Chloe has also had plenty of Ship Tease with Regina in JN087, as the two become closer. The two became instant friends and were so close that they even wrote letters to each other regularly even after Regina transferred schools again.
Chloe also meets and befriends Serena in JN105. Chloe and Serena have a ship tease moment while they are shopping for Contest Spectacular outfits, especially as they are looking at suitable outfits in the mirror. At the end of the episode, Chloe reminds Serena of the words she told her when the latter is contemplating whether she should accept Lisia's proposal to form an idol unit, and the two hold hands and laugh.
Two different posters showcase Chloe with the girls she has met: one showcases her with Dawn, while another shows her with Serena and Lisia.
JN085 reveals Korrina and Bea are friends, and Korrina apparently has the habit of hugging Bea. Goh and Ash initially assumed they disliked each other, especially after Korrina ran in Bea's direction without warning and with clenched fists.
JN138 has Ash's Corphish and Misty's soon-to-be Clauncher stare at each other intensely. While this would be normally unremarkable as they stare there are hearts in the background◊ and the episode confirmed earlier that they're both male...
Manga
The final chapter of How I Became a Pokémon Card features two boys who have a very close friendship and constantly blush around each other; it doesn't help that one of them is a trans boy, and his friend didn't believe him in all his years he knew him.
In the FRLG arc, fans have taken to pointing out that Green is Red's coathanger.
Gold and Silver had some rich 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.
Black and Cheren have this too, with Cheren even having an explanation for how Black's mind works, the two blushing around each other, Cheren's entire life goal to be to support Black's, the list goes on. Notably, the Legendary Pokémon Reshiram awakens as a result of Black's fury over Cheren being manipulated. Black even bridal carries Cheren (with Reshiram behind them) as he enters the final battle with Team Plasma.
Magical Pokémon Journey does have Squirtle who has a crush on Almond. Charmander is quite obsessive about Eevee and is implied to have a crush on him.
Satoshi and Shigeru in Pokémon Zensho have the same Foe Yay Shipping motivation 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.
Video Games (general)
You can literally invoke this to most of your Genderless Pokémon! If you bring one (like a Metang) to a Day Care Center together with a Ditto (another genderless Pokémon), you will eventually receive an egg containing a non-Ditto baby (for this case, Beldum).
You can also invoke this in Pokémon-Amie with the corresponding gender.
Red and Blue. Blue's description of having been your friend gone rival makes him sound Tsundere toward Red, you have Foe Yay Shipping subtext for most of the original games, and once you go back to being friends he seems to think about him a lot. Furthermore, Blue seems to be one of very few characters (if not the only one) In-Universe that actually understands Red's Visible Silence.
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 FireRed/LeafGreen these are unchanged if you play as Leaf.
At one point in Pokémon Let's Go, Pikachu! and Let's Go, Eevee! Trace gives you an item. Doesn't sound too suspect, but the way he does it (slowly approaching you and the screen suddenly going dark just before he makes contact) makes it look like he's about to kiss you instead.
The original Gold, Silver, and Crystal contain a strange glitch-induced example. Kurt could make you several unique Poké Balls with unusual effects if you gave him Apricorns, but many of these balls were glitched to have effects different from those intended. One of these balls, the Love Ball, was a Situational Sword intended to give a catch bonus if the targeted Pokémon was the same species and opposite gender of the player's (presumably to show off the then-new breeding mechanic)... but the bug caused it to get the bonus on Pokémon of the same gender instead. Buggy Ho Yay ensues!
At one point in HGSS, Blue calls you up, and comments on how he misses Red and you remind Blue of Red. (He seems to be crying while he tells you this.) He then goes on to wonder what Red is up to on Mt. Silver.
Sr. and Jr. Anna & Meg. 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.
Lisia 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 remakes, 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.
This, and his strong relationship with his first Pokémon and team ace (A male Gardevoir in R/S/E, a Gallade in the remakes), both Pokémon renowned for the bond with their Trainer.
This conversation between an Ace Trainer and a Delinquent you find in Mauville City, both female. If nothing else, it sounds like a breakup:
AT: "Eh? Seriously, ma'am? Ya gonna treat me to dinner?"
D: I told youse I would, eh? Ya managed to become an Ace Trainer, doll. We gotta celebrate somethin' like dat. Pile up as many o' dem Village Sub Combos or Magnemite Croquettes as ya want.
AT: Thank's ma'am! I'mma take you up on that!
D: Yeah, kid. You do dat. But dis'll be our farewell meal, y'unnerstand? Youse can't keep hangin' out wit' a hood like me- not even one with a fab do like mine. Not wit you bein' an Ace Trainer an' all.
AT: M-ma'am...
Like noted above, the characters are given a little bit more personality and hints of their relations with others in the remakes. Some of it stays All There in the Manual or is integrated into the dialogue in reasonable ways, such as Flannery saying she heard about something from Winona. Then Brawly shoehorns Granite Cave into his after-battle conversation seemingly so he can point out how "my friend Steven" rushed there after being told about it. (The German version somehow adds to this despite translating the above quote as "meinem Bekannten Troy" - unlike "Freund", Bekannten could mean boyfriend regardless of grammar issues.note "Ein Freund" is always accepted as strictly platonic. "Mein Freund," though literally the possessive form "my friend"... People learning the language are typically recommended to use "mein Freund" and its feminine form "meine Freundin" sparingly (if at all!) to avoid accidentally calling people their girl/boyfriends left and right, despite the term technically being ambiguous.)
It's hinted at that Steven and Wallace are closer than first thought. At the end of the Delta Episode, one of the many cutscenes show Wallace talking to Steven at the Pokémon League. Steven says he needs to learn more about the world, and asks Wallace if he will be by his side when he does decide to pursue his dreams. Wallace says he will be there when the time comes.
The official Japanese Pokémon Twitter account has posted this, regarding Archie and Maxie's relationship. A rough translation of the last sentence: "Somehow, their relationship seems pretty good!"
In the ORAS demo, Matt tells Tabitha that he thinks he's funny, and he loves funny interesting dudes "like my bro, Archie!". Right after that homoerotic sentiment, Matt tells Tabitha that he's gonna love him to bits. Okay, Matt.
One pairing that seems more hinted at than others would be Gym LeaderVolkner and Elite Four MemberFlint. Volkner grew up in a Friendless Background, and the lack of challengers at the Sunyshore Gym made him Go Mad from the Isolation, plunging him into depression. In his adult years, the only person he ever had who he considers a friend is Flint, who served to be the beacon in his dark path by inspiring him to be the best Gym Leader of Sinnoh. From this, Volkner and Flint grew to be life partners, and even in the anime, they're shown to be extremely intimate with each other, almost to the point of romantic interest.
The Ferris Wheel Date Moments 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 Pokémon 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).
One of the male backers in the Small Stadium will claim that he "wishes that the athletes would fight over him the way they fight over the ball". This is the case even when the athletes in question are the male Hoopsters instead of the female Smashers.
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...
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.
Also, after the butler watches you and Shauna, he gives you TM17, Protect. Even the butler can sense it.
There is a Brains-and-Brawns Double Battle formation with a male Martial Artist and a male Psychic trainer (Trainer names Frank and Sly). 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.
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.
Sycamore: What a passionate person. He's just like a blazing flame.
One of the trailers for the game showed an older Red and Blue hanging out together by Alola's new Pokémon League. Fans immediately decided they had come to Alola for their honeymoon. It doesn't hurt that they have dialogue reminiscent of Like an Old Married Couple...by which we mean Red says "..." and Blue says "As silent as ever, eh?"
If you choose to play as a female protagonist, many of Lillie's interactions with the player character can come across as this. The most blatant case is during the credits sequence, where she appears to be about to give a Love Confession before being interrupted by fireworks.
There's also an earlier scene on Exeggutor Island where the two of you end up in a cave together seeking shelter from the rain, where Lillie is also about to say something very very personal to you when the rain stops. Then, big giant rainbow.
Many fans have noticed that Burnet (Kukui's wife) physically resembles Guzma (Kukui's old friend). Kukui has a type indeed.
For most of the game, Gladion treats Hau as a carefree idiotic boy who can't take things seriously....only to reveal to the player at the port that he considers Hau an “interesting kid” and that it’s admiring how he doesn’t feel overshadowed about being Hala’s grandson.
Also, regarding Gladion. For some reason he's perfectly fine with Lillie and the protagonist's constant Ship Tease but gets angry after Hau praises Lillie's new outfit.
At the Poni Plains there is a Male Ace Trainer (named Cole) who gives out the TM for Quash and after defeating him he will refer to the player as "babe" and "baby" regardless of their gender.
There's this line Gladion says to the player (regardless you play as a male or a female) during the Champion Challenges.
"What does a Pokémon Trainer really need to be successful? I guess everyone might have their own answer. But for me....I want the strongest rival for myself."
When the player reaches Po Town, they can find two Team Skull Grunts waving at each other from opposite sides of a hedge. The first one waving will say "What's wrong with that guy!? Doesn't he realize we're being invaded!?" The Grunt from the other side? "What is wrong with him?! Why does he keep on staring at me? Does he see how hot I am or something?!"
Also in Po Town, if your character is a girl, one of the female Team Skull grunts on the roof will ask if you're "looking for a battle in a romantic spot", and another pair of female grunts inside the main building will have their conversation interrupted when you walk in on them in their room, realizing that your player character is pretty cute (they get angry instead if you walk in on them with a male player character).
Hapu outright forgets to give the player a ride Pokémon earlier in the game due to being "taken aback by Lillie and how lovely she was."
In the post-game, Sonia is absolutely distraught when her (female) lab assistant hands over Wishing Stars to Sordward and Shielbert, her stint for the professor having been an infiltration mission. She tells Sonia she's sorry, and Sonia tearfully asks, "Was everything...was it all a lie, right from the start?" with the implication their short-lived bond was something more special assistant and professor.
Pokémon Camp as a mechanic is ripe for this. Because of how much your Pokémon getting along with another Pokémon is based on Nature and how much time they have spent together within your party, it can easily create Pokémon that get along with Pokémon with the same gender while rejecting Pokémon with the opposite gender. The text that appears implies this as well, with relationship statuses stating that two same-gender Pokémon "seem very interested in each other", "seem to be drawn to each other", "seem to trust each other" etc.
Possibly the whole story on how Galar came to be! If you look at the tapestries in Hammerlocke, it seems after they defeated Eternatus, they got married, then ruled the kingdom together, and broke up after Zacian and Zamazenta fell asleep.
Circhester City has an area called "The Hero's Bath", a hot spring where both the heroes were said to bathe in to heal. Possibly at the exact same time.
It's further implied in the post-game, where one of the player character's choices after defeating Sordward/Shieldbert for the first time is "I'm worried about Hop...", that if you're playing as a boy, you're worried either due to him being your childhood friend, or something more...
During one of your art classes, the teacher, Hassel, invites Brassius, the Grass-type Gym Leader and a fellow artist. During Brassius' lesson, he tells the story about how Hassel helped him get out of the depression he fell into that was causing him to lose the will to create. They refer to each other as "Brassie" and "Hass", and Hassel is moved to tears by Brassius' speech and how kindly he speaks about him. Hassel's storyline is about him deciding to be a teacher and an artist despite his very traditional Dragon Tamer family wishes, since they want him to quit his current job and be the leader of the family in his aging father's place; Hassel picking art and teaching along his male companion/best friend parallels stories of some real-life queer artists who chose to sever ties with their families and their expectations of fulfilling their gender roles to create art with their same-gendered lover. As icing on the cake, Hassel's Elite Four team features a Flapple, which is a Dragon- (Hassel's preferred type) and Grass-type (Brassius' choice) - Sword and Shield establishes that in Galar, giving someone an Applin (Flapple's pre-evolution) is a romantic gesture.
Eri's friendship with Carmen, a female team Star member might come off a bit like Carmen is in love with Eri- she used to bully Eri because she was "prettier" than she was, but instead of being mad at her, Eri behaved very kindly and even invited her to be a team Star member, which Carmen chose to do, and now has nothing but good things to say about her commander. It certainly comes off as Carmen bullying her crush and then being openly infatuated with her, enemies to lovers-style.
The relationship between Guildmaster Wigglytuff and Chatot is far more than platonic. At first it seems Chatot's apparent crush (from travelling with him for so long and respecting him) on the Guildmaster is one sided as Wigglytuff seems apathetic to the idea of spending time with Chatot on the expedition. However, when Chatot risks his life to save Wigglytuff, Wigglytuff is in tears and tries desperately to help him. It happens again when the player and partner get attacked by Kabutops. Wigglytuff is just barely holding it together and calls Chatot his invaluable partner, to which Chatot is delighted to hear it. It's implied Wigglytuff nursed Chatot back to health after the heroes leave for the Hidden Land.
Speaking of the player and the partner, depending on their gender, the game plays out like a love story/triangle between them and Grovyle too, who seems to trust each other more than anyone else. Grovyle even says "Parting hurts" which could be taken as the loss of their significant other. The player/partner relationship is played out like a couple in that everyone seems to call them the greatest of combinations, the Partner cries a river when the player Disappears into Light, the Partner constantly tells the player how much he/she gave him/her strength and can barely keep it together when the player supposedly disappears forever. They even play mommy and daddy to the baby Manaphy and are very concerned when the player seemingly gets trapped in a nightmare made by Darkrai.
At one point, the player encounters a male Swimmer spying on Rachel and Sawyer. The player asks if he's a Rachel fan, and he says no, he's a Sawyer fan. The Swimmer then proceeds to gush over Sawyer's body for the rest of the conversation.
One particular event opens with Red and Blue conversing, and deciding to go off together to Oak's amusement. Then, Steven and Wallace repeatedly talk about what great friends they are, and how much they value each others' input, and both end up lavishing praise on Grant's rock accessories and how attractive and stylish they are. Not that much on its own? Well, any subtext is compounded by the fact that all this happens in the event that began on Valentine's Day.
Whitney's lines about "the girls and the Pokémon [all being] so cute" and having "a whole lot of special someones" carry heavy shades of this, especially when you remember that her gym is populated exclusively by women in Pokémon Gold and Silver. Kris saying that she's cute also makes her extraordinarily happy, to the point that she stops crying over the battle she just lost.
The Ideal Formula story event has outright stated that Hilbert is the one who N faced. And the event has outright stated that Hilbert has been looking for N in the sequels. It doesn't help that Hilbert had been talking about N so much that Hilda instantly recognizes him when he landed in Pasio, despite never meeting him up until that point. N has also stated that he has thought of Hilbert during his travels and Hilbert keeps referring to N as an important friend. The end of the event has a sincere moment between N and Hilbert where N pretty much has promised not to say goodbye anymore, all while the two are standing together on the shore, watching the waves in a manner that feels very couple-y. Bianca even happily states that they "finally got Hilbert and N alone together", giving Shipper on Deck vibes. Not to mention the game's official twitter account released artwork like this and the best medal you can get for it is called "N-Describable Love".
N and Hilbert get even more of this during the second anniversary gala event; when N asks the player character to act as his opponent for the gala, Hilbert and Hilda both immediately show up to take offense to this, and even briefly bicker amongst themselves over who gets to fight N instead. Almost makes Hilbert come off as a Crazy Jealous Guy.
Also during the anniversary gala, one of the things N can say to you if you speak to him while he's idle is "If you love someone and they're present to hear it, please tell them. Don't make the same mistake I made." While he doesn't name any names, it's easy to connect the dots and assume he's talking about Hilbert.
In the Unova Chapter of the Villain Arc, a lot of emphasis is placed on how strong N and Hilbert's bond is, with N noting that his "heart was pounding" when Hilbert trusted him with his Kyurem and how he wonders if this is what it feels like to trade Pokemon with others. Again, the official Twitter account got in on it too, with the Japanese version even saying that Hilbert trusted his feelings to N.
Other
There's a series of board books based on the franchise dubbed "Pokémon Tales" that came out in the 90's. One of them, "Squirtle Comes Out", is about a Squirtle whose friends coax him out of his shell so that he can view a rainbow with them. The last two pages show Squirtle happily gazing upon the rainbow, saying "Wow! I'm so glad I came out!" Naturally, the internet had a field day with it.
, where Seymour hugs Ash for saving him.
