Do you know about that girl in Sootopolis who gives you berries daily? Similar to what happened to Mew in Red and Green, Kiri's an NPC added just before the Japanese release of Ruby and Sapphire in honor of the birth of Junichi Masuda's daughter, who the NPC is named after. And then, just before she gives you a berry, she says this: "My mommy and daddy named me that so I would grow healthy and warmhearted. That's what they wished." Even better, this is one of the few speeches that was completely unchanged in the remakes.
Post-Emerald. Despite their previous animosity towards each other, Archie and Maxie put aside their differences and quietly return the orbs, leaving together.
When you walk into Steven's house and you see a Pokeball with a letter aside it. In the letter, he mentions his busy schedule, asks you to take the Beldum, which is his favorite Pokemon, and says "may our paths cross someday." It's pretty sweet for someone to give you a gift of their favorite Pokemon.
Omega Ruby and Alpha Sapphire
Several meta examples:
It is◊ possible◊ for the first time in ten years for a Pokémon to return to the region it originated from after being transferred a generation forwardnote excluding Gold and Silver and their remakes. Even better, should you bring one of your Old Hoenn Alumni to visit the Gamefreak staff, they will give you a special certificate◊ to commemorate your dedication to your old partner, which can be used as Wall Art to decorate your Secret Base.
The Pokédex has been redesigned to resemble a Game Boy Advance, emanating a wonderful sense of nostalgia.
Evolving Bagon to Salamence becomes even more heartwarming now that it has a Mega Evolution. Mega Evolution requires having an exceptional bond between trainer and Pokémon, so being able to take Salamence's dream for flight further by Mega Evolving it to a more aerodynamic design is just moving.
Norman bows in respect to you before the Gym battle begins. No other Leader shown does this - they all take battle poses instead. Even before the player wins, Norman is still incredibly proud of his child. Aww.
When you beat him, it says that the player gets a badge from "[their] dad". Not from the Gym Leader. Awwww!
After you beat Norman, Wally's dad and him share a moment in which they agree that seeing their respective children go off on their own adventures makes them both happy and sad. More aww.
While the special anime trailer for the game is mostly showing off the region's Mega Evolutions, we get to see a really cute relationship between the three starters and May and Brendan. Watching Brendan's Sceptile give him a friendly nom on the head or Blaziken lightly headbutt May because it wants to be pet is nothing short of adorable.
Wally had been given more love within these games, as in addition to gaining his own theme song, he gained his own epic Metal battle theme. He's also one of the only trainers to gain a Pokémon with Mega Evolution, a honor usually reserved to trainers important to the plot. In addition, after the events at Mt. Chimney, Wally gets listed as a certified trainer within all Pokémon Gyms. Including the ones you had defeated up to that point. This shows just how much he has grown as a trainer.
Not only this, in the Gyms from Lavaridge Town onward, his name appears before yours.
The child on Route 104 who says he should have bought a Potion because his Pokemon is running low on health returns. Except if you have a Potion, you actually have the option to give him one of yours. There's no reward for doing so, but it's sure to make you feel warm and fuzzy inside.
The final door to the Champion reminds the player of how far they have come on their Hoenn journey.
What unfolds after you've completed the Delta Episode are a series of very touching events:
First, at the Space Center it's confirmed that the meteoroid has been destroyed, and they celebrate.
Wally comes home to his parents in Verdanturf Town, and after he leaves they know how happy he is.
We then come to Steven having a chat with Wallace in his Champion Palace about how there is much of the world he wants to see thanks to what you've taught him, implying a 10-Minute Retirement as Champion.
Following that is Zinnia and Aster in Meteor Falls, talking to her grandma about what can come from life.
We come to your parents and Brendan/May's talking about how happy the latter must feel to have you in their life. But the last bit is the icing on the cake - You and Brendan/May are on your date at the Mossdeep Space Center, as they get something for you at the concessions, then take a picture pretending to be on the moon in a space suit, and afterwards you've watched the Litleoids. Yes, for the first time in the entire history of the main games, a romance explicitly blossoms, between the player and rival no less, meaning both they and the normally completely characterless player character confessed their love for eachother offscreen. They thank both Norman and you for it, feeling happier than ever. You both then return to Littleroot Town, but they happily say "See you tomorrow!" before entering their home. As you enter, your parents welcome you home too, wrapping up this beautiful piece.
After you become Champion, it's revealed that your rival acquired their own Mega Bracelet. After the credits roll, and before the Delta Episode, you get to have a battle with them, and they Mega Evolve their starter. The lengths they went to in order to try to become your equal is beautiful.
After you win a Contest, go out into the front lobby and you will find a small crowd of adoring fans waiting for you, who talk about how amazing your performance was and give you berries/healing items/valuable items to help your Pokémon get even stronger or more beautiful. Even if you don't win, at least one or two fans will be there to encourage you and tell you that they loved your performance.
It gets better: Win enough Contests in a row and everybody in the Trainer Fan Club in Lilycove will adore you unconditionally, including a little girl who asks you to shake her hand ("Yaaaaaaaay! I'm not gonna wash my hand today!")
When you run into your partner, occasionally they get tongue tied in shyness while trying to ask if you would like to walk with them to a town. It happens after Meteorite Falls, and again after getting the badge from Flannery.
The Safari Zone has a bit of this. There are plenty of people there making sure the Pokémon there are happy, healthy and fed. However, the Safari Zone doesn't charge admission for entry anymore. So all of these people are going out of their way to make sure these Pokémon are fine and get loving homes, entirely out of volunteer work.
After you catch/beat your game's legendary, the villain teams make up and vow to create a better world another way.
And a little before this, there is a montage of the people from all the towns around Hoenn looking up at the bad weather being dispelled and gives off a real hopeful feel. Followed by the player leaving the Cave of Origin to be congratulated by both teams, Steven, Wallace, and May/Brendan.
An easy-to-miss scene during this part: you can see Wally looking up at the sky, too... and he's already at Evergrande City. It's equal parts heartwarming and awesome, since it's yet another example of just how far Wally's managed to come as a Trainer.
You're also told that the events caused Kyogre or Groudon also changed the Hoenn region profoundly in a good way: the number of Pokemon species that can be found in Hoenn increases dramatically, leading to an even more diverse ecology (and many many more Pokemon to catch).
In the Battle Resort, you encounter a Magma Grunt and an Aqua Grunt who ran away from their respective teams to be together. When you first arrive, the Aqua Grunt's immediate response is to distract you so her beloved can escape, while the Magma Grunt refuses to run away. Then they learn that Team Magma and Aqua have reconciled from their friends, who wish them well before leaving the cottage.
And if you go back and talk to the two ex-Grunts, they'll ask you take their Camerupt and Sharpedo, respectively, as a request to take care of them because they no longer have any use for their Pokemon.
Archie and Maxie are probably the only team leaders that actually, 100% care about the members of their team as well as their cause. They are both very close to their Admins, though Archie's friendship with Matt and Shelly is more apparent. Also, they are the only leaders legitimately concerned about bettering the world for everybody (Cyrus and Ghetsis fooled their teams for their own selfish goals, and Lysandre only cared about the "beautiful" people.)
Elite Four rematches: they all acknowledge that you are a Champion and thus their attitude to the battle is far more relaxed. The fact that this game is the only Pokémon game which the Elite Four acknowledges you fully can be considered as heartwarming.
Before heading off to Sootopolis, your game's opposite villain team leader will apologize to you for the catastrophic events that you have to fix for occurring. Even though the protagonist is an incredibly prodigious Trainer by design, it's kinda nice to have the fact that you're still just a kid be addressed.
Small, but worth mentioning. OR and AS's respective team leader's dialogue for when you first meet the legendary in the Magma/Aqua suit is slightly different. While Maxie will tell you not to waste a single second, Archie will reassure you to not be afraid.
Archie in general does this- he subtly encourages the player to be strong, is regularly impressed with you, calls you scamp/scampo, and the way he talks gives the feeling like he's your Boisterous Bruiser of a big brother looking out for you.
There's also the dialogue from your villain team's leader if you go back to their hideout after the Delta episode.
Maxie, in Omega Ruby: We will always welcome a visit from you.
Archie, in Alpha Sapphire: Make yourself at home, all right?
Another meta example, courtesy of Spacebattles. A space-battler comments on winning the Master-rank Beauty contest with Mega Rayquaza:
"But is it any surprise? A divine dragon who looks over humanity from the heavens, taking on the hopes and prayers of a better tomorrow and appearing as the shining avatar of salvation when all hope is lost to the world... Could anything be more beautiful?"
Your Secret Base pals actually help you find flags for your base - there's a chance that they'll give you free flags they found if you were to talk to them.
While most legendary Pokemon have a sense of honor and would rather battle you first to see if you're worthy of being their partner, Latios and Latias want to join you on your adventure because they like you that much.note It only goes for the one you encounter with Steven, though (Latios in OR, Latias in AS); the one you encounter with the Eon Ticket event will want to fight you.
In Sea Mauville, one of the trainers you can fight are a pair of Mysterious Sisters. They seem paranoid in that they apparently believe you're out to separate them, but it's touching to see them caring so much about each other.
When you accidentally select your rod or bike, where normally the regional Professor will tell you it's not the time or place for that, your father's voice will deliver the speech instead. In a game franchise where fathers are rare, it's sweet to see a protag whose father means enough to be the one to give those words.
Zinnia opening her heart up to you when you reach the Dragonhark Altar. Crosses over with Tear Jerker, especially when you say that you too have had to hold back your tears at one point.
When you become the Champion, the BuzzNav people will talk to Professor Birch about you. He's apparently so close to the family he actually used to change your diapers, which is equal parts embarrassing, amusing, and weirdly heartwarming.
Your main rival character (Brendan/May) tend to evoke this. They want to stick by your side and if they can't be beside you, they're right behind you, supporting you, always. Unlike Calem/Serena, they're not even frustrated or disappointed that they can't beat you. Well, maybe a little bit disappointed, but like with Norman, they're also very proud of you and proud to call you their friend. Simply put? They love you unconditionally, and it's heavily implied (especially for Brendan, who's not as adept at hiding his feelings as May) they have a crush on the player. ... Until, shockingly, it's outright confirmed after the Delta Episode, as mentioned above.
The end credits sequence. You and your rival go home together, accompanied by a beautiful, peaceful medley of the original RSE end credits theme with various town themes. Throughout the sequence, various scenes are shown with your own Pokémon in key battles throughout the story, so the player can reflect on how far they and their Pokémon have come.
In Shelly's room in the Aqua hideout, one can find an old picture of two kids smiling happily with the legendary Pokemon, Jirachi. These two kids are strongly implied to be Archie and Shelly themselves... it seems like their love of Pokemon goes a long way back.