In the Devon Corporation building in Rustboro City, there is a scientist who mentions that "I'm attempting a device that lets you see into the dreams of Pokémon!! But it's not going well..." Two generations later, you get to do just this in Pokémon Black and White. This is referenced to in the remakes.
As mentioned in Red Herring on the main page for this game, the Winstrates discuss how good and awesome their son is, but he is simply nothing more than another Cooltrainer on Victory Road. Like how someone is the village's best swordsman, but will find themselves to be average in the grand scale, the cooltrainer comes off as talented to the Winstrates since he is the best in their family.
Gardevoir's loyalty and devotion makes sense from an evolutionary (Darwinian that is) standpoint if you look at it's pre-evolved forms. Ralts is one of the weakest Pokemon in the series, even outdoing Magikarp and Kirlia is the weakest evolved Pokemon that isn't a sedentary cocoon. Gardevoir evolved to fiercely protect those it loved, their children, as they were so vulnerable. And think about humans, they can't fly, shoot fire or attack with their minds. Gardevoir sees it's trainer as a defenseless child so the instinct carries over.
Who happens to be the main trainer in Gen 3 to have a Gardevoir? Wally, the Ill Boy, easily one of the most vulnerable major characters in game. (He had a Gallade in the remakes, a Pokémon known for fighting fiercely when protecting someone.)
A meta example. In the games data, there exist NPC graphics for an odd yellow-skinned man. This scared a lot of ROM Hackers, and some were confused of why it was there, much less what it was. Turns out, this was a character from Game Freak's first game, Mendel Palace!
Absols always show up before major disasters, attempting to warn people of them. Where do Absols show up in the game? In the routes between Fortree and Lilycove. Right before Magma/Aqua steal the orbs from Mt. Pyre and resurrect Groudon/Kyogre.
Mega Blaziken was in Pokemon X and Y, while the other Mega Evolved Hoenn starters have to wait until Omega Ruby and Alpha Sapphire. Get it?
The last or omega Hoenn starter listed is Mudkip, who as a Water-type has a better time against the Ground-type Groudon. The first or alpha Hoenn starter listed is Treecko, who as a Grass-type has the advantage against the Water-type Kyogre.
Omega Ruby and Alpha Sapphire seems weird to most people that it's like put like that instead of the other way around but this cause two bits of brilliance. 1) Their acronym Oras, has the Bilingual Bonus of being Lithuanian for weather. and 2) All life started at sea but ends up on land.
Two critical locations are Mt. Pyre and Cave of Origin (on the former one there are weather trio Orbs, at least the two related to Groudon and Kyogre, the latter is where you fight the legendary as part of climax). The former is a graveyard, the latter is a place about which it's said it's where life begins (hence its name). Beginning and end. Alpha and Omega.
Continuing on with the Omega/Alpha theme- Primal Groudon has the ability Desolate Land (Land of Endings in Japanese), which sounds like a place where life would end (hence Omega). Primal Kyogre has the ability Primordial Sea (Sea of Beginnings), which sounds like a place where life would begin (hence Alpha). Furthermore, their signature moves Precipice Blades (Precipice refers to the sharp drop at the end of a cliff) and Origin Pulse (Origin and beginning) also reflect this.
Their abilities also reflect the goals of the villainous teams trying to use them. Desolate Land for Magma, and Peimordial Sea for Aqua.
Mega Swampert having Swift Swim seems pretty random at first considering how bulky it is, but a closer look at its design shows that it's actually a perfect fit for its ability. Its overall design is more streamlined than before, its wider frame means it gains more lift as it swims, and its arm muscles are much stronger, making Mega Swampert a very good swimmer. Not only that, but this clip shows that those orange bumps on Swampert's arms can hold and eject water at high speeds making it move faster. Now in what weather condition is there a lot of excess water in Swampert's surroundings for it to use?
Why does Mega Sceptile have Lightning Rod? Its tail looks like an evergreen tree and the tip of its tail looks like a lightning rod. A common way to protect trees from lightning strikes is to put lightning rods on them to absorb the electricity.
Both Mega Swampert and Mega Sceptile's abilities are particularly useful in double battles. Fitting, given the original games were the first to introduce them.
Some people might think that it's a little odd that the Dragon-type Altaria had the Fairy-type Moonblast added to its movepool in X and Y given the relationship between the two. Come ORAS, and Altaria is given a Mega Evolution that renders it Dragon/Fairy. It's also no wonder why it lost it's secondary Flying-type - calling it a living cloud doesn't even begin to describe the sheer amount of plumage it has.
Team Magma and Aqua's designs in the remakes serve to make them more obvious Foils to each other than the original games. This is especially obvious in the admin and leaders' designs. Courtney is dressed conservatively while Shelley's uniform bares her midriff and has gaps that expose her skin. Tabitha is overweight and fully dressed while Matt is muscular and doesn't wear a shirt. Maxie has a slim, intellectual design while Archie has a muscular, athletic design.
While Mega Salamence's design at first can seem quite hilarious — and many have found one or another reason to pick at it — it actually makes quite a lot of sense, design-wise. Ever since Salamence was a Bagon, all it wanted to do was Fly. Now it's Mega Evolution makes it heavily resemble Latios and Latias, who are often compared to jets, showing that not only can it fly, but it speeds through the skies at the same time. Bringing out Salamence's true power only helps further realize it's dreams.
Mega Diancie has a drop in Defense and Special Defense after it Mega Evolves from Diancie. Mega Diancie has lost all its impurities and become all diamond and diamonds maybe one of the hardest substances, but they're so brittle, that if small enough, they can be shattered with a hammer.
Mega Metagross is this. It looks like they added a Metang and two Beldums onto a normal Metagross but that's the brilliance. Each evolutionary stage of the Beldum line is said to be composed of two members of the previous stage. Metang is two Beldum and Metagross is two Metang or four Beldum or one Metang and two Beldum Mega Metagross is still technically two normal Metagross combined.
Mega Audino resembles Audino's equivalent of Blissy. This doesn't make sense, until you remember Mega Banette. Mega Banette could have easily been a regular evolution to its line like Dusknoir was but it would not make a good foil if it was. Mega Audino is Audino's answer to Blissey while at the same time giving a difference between the two Pokemon so that the two make good foils for one another.
Why on earth would Wattson entrust a little kid with the New Mauville generator? Because you have beaten him, proving that you're at least somewhat responsible - and because it is much easier for you to reach it than for him! In Gen III, non of his mons could learn Surf (and even in the remakes, the chances that he'd have a Raichu with Surf are slim), and the landscape would be harder to traverse for an old, chubby man than for a youngster like the protagonist.
Ok, stuffing more than 30 legendaries in one set of games might be a tad overboard. But if you take into account that exlcluding the Poke Bank Celebi X and Y only offer 7 legendaries, the fact that almost none of the official tournaments allow Pokemon that were transferred from previous generations, and since that method was the only way to bring most of the legendaries in the series into Generation VI, this actually might shape up to be a pretty convienient thing for many players - allowing them to use most of the legendaries they couldn't use before ASAP instead of spreading the pool over multiple sets of games outside of the generation's primary set. Not to mention that due to the coding in the Gen VI games that allows mons in the "No Eggs" group to have no less then 3 I Vs of 31 when generated in the wild, all of these legendaries are almost guaranteed to be competitively strong.
Mega Latias and Mega Latios are confirmed to look exactly the same as they do in X and Y's hidden data. In other words, they're difficult to tell apart. Not only does this make sense given that they're alternate gender counterparts to each other, it also makes sense from a developer's viewpoint due to the fact that it allows the developers to represent both using one overworld model when you use the Eon Flute to fly on them in real time (instead of instantaneous like using the Fly HM move).
The lack of character customization in Omega Ruby and Alpha Sapphire makes perfect sense when you think about it. In Kalos there is really only one route required for Surfing (outside of Victory Road). In Hoenn, nearly half of the region is water with numerous spots for Diving and such. The updated outfits for May and Brendan look like swimwear. Most fashions in Kalos go for looking good and would probably not be practical for Diving or most clothes would probably be ruined if you did.
The influx of Kanto-only Pokémon with Mega Evolutions in Omega Ruby and Alpha Sapphire seems out of place at first, considering they're suppose to be remakes of Generation III. Then you remember that Generation III also includes FireRed and LeafGreen which took place in Kanto, meaning this way all of Generation III can be represented.
When Team Aqua and Team Magma are feuding at Mt. Chimney, a lot of the members have Poochyena with them, and, in a neat little touch, these Poochyena seem to understand their masters' goals; the Team Aqua Poochyena, when spoken to, say "Bushaa!" (which sounds like water gushing when spoken aloud) and the Team Magma Poochyena say "Bufoh!" (which could reasonably sound like a volcanic eruption).
Episode Delta backs to Hoenn's history 3000 years ago, and involves Deoxys. Ruby and Emerald's entries say it was a space virus that got exposed to a laser beam. Now what kind of laser beam would be used 3000 years ago? AZ's weapon is something along these lines.
The Version exclusives between the Dual Legendaries makes sense if you go by the respective colors of Ruby and Sapphire. They are exclusive to a version according to their own color or variant:
Ho-oh is mainly orangey red, while Lugia, while mainly white, has light blue and navy as part of its color scheme.
Palkia has pink, while Dialga has navy and cyan as part of its color schemes.
Reshiram produces an orange flames when activating its ability. Zekrom produces Blue lightning by doing the same.
While Tornadus is green instead, it's still exclusive to Omega Ruby by process of elimination and was originally going to be red. Thunderus, being cyan in color, is exclusive to Alpha Sapphire, as Tornadus goes to the other.
In Emerald Version, Groudon and Kyogre would be simultaneously raising the land and sea. They aren't going to destroy or expand the world... they're going to remake it. All structures on land will crumble, human kind will fall, oceans will reshape continents. It's not the end of the world. It's the remake of it.
The Delta Episode finally revealed the existence of a Pokémon multiverse. Using this fact, it's very easy to prove that all Pokémon media and all Pokémon games are canon even if they're remakes, they're different "versions" of each other or that they contradict each other - they just portray events from different universes.
The theme for the Primal Legendaries contains snippets of the original GBA song from the original games. In other words, the song is reverting itself.
Overlapping Brilliance and Horror alike, why would the special DexNav encounters be so powerful? Egg Moves, Hidden Abilities, rare (and often man-made) hold items, up to a minimum of 3 perfect IVs... It all adds up! They're all breeding rejects, the countless pokemon hatched and released by other players in the pursuit of eugenically-superior competitive pokemon! They cling to these hold items because it reminds them of their time spent in the company of humans, and lurk near where trainers travel in hopes of meeting someone who would adopt/capture them!
When you are underwater, weather abilities somehow work. Underwater. Especially when a Water-type, like Kyogre, has Drizzle as its ability, and it rains underwater. Or, perhaps more baffling, Primal Groudon's ability, which negates water attacks. Underwater.
On a similar note, when flying on the back of Mega Latios/Latias, one can engage in midair battles against flying wild Pokemon. You can use Pokemon that can't fly for this. Even more confusingly, it also works with the Lati you're supposed to be riding, and they don't start out in Mega form to boot.
In this generation, no message is given when you lose a Pokémon battle. You are simply told that you whited out - and then wake up in a Pokémon Center. It's either a Fridge Horror... or Fridge heartwarming because the person you were having a battle with dragged you all the way to the nearest Pokemon Center even if they did take half of your money
Team Aqua wants to flood the earth. Team Magma wants to cause droughts and dry up the land. Both of them unleash a creature that can do that and proceeds to begin to do so in a wildly out of control manner. Now imagine if you weren't there to stop said creature.
Ralts are extremely rare. When you meet them, they are at a level where they have no offensive attacks, and are surrounded by bug & dark pokemon, whom Ralts are weak against. It's likely they they are close to being wiped out.
Your final fight with Wally is a lot more tragic when you realize how much he idolizes you and wishes to fight you. To make a comparison, it's the equivalent to a sick kid making a wish on the Make A Wish Foundation to play basketball with their favorite athlete... Except that said athlete doesn't hold back, use underhanded tactics and (possibly) smack talks and showboating. How does victory taste?