The remakes give the Koffing family for Team Magma to use, and the Grimer family for Team Aqua to use. Both are fitting additions, as the Koffing family is gaseous, almost like the smog or ash from a volcano, so it makes sense that Team Magma would use them. Meanwhile the Grimer family is more liquid based, kind of like the water in the ocean, so it makes sense that Team Aqua would use them.
Why did Maxie and Archie fail in the original games? They wanted to control Groudon or Kyogre... with the Orb of the opposite legendary. As the remakes reveals that both Orbs have different effects on both legendaries, what the team leaders wanted to do is to suppress the Pokémon enough to be tamable.
Alternatively, the Orbs did correspond with the right Pokémon. If you look closely, Groudon has blue Tron Lines, so the Blue Orb would probably match its inner blue aura. The same can be said for Kyogre who has very noticeable red Tron Lines, so the Red Orb would likewise match him. Maxie and Archie couldn't control them because, well, man is no match for the power of nature when things start to really hit the fan.
The remakes extend upon this: the matching color Orb awakens the legendary, but the opposite color Orb keeps its power in check, so the villains should have taken both Orbs, but only took the matching Orb because they didn't realize the true extent of the legendary's power. You're given the opposite Orb after the Mt. Pyre event and the matching Orb after encountering and catching/defeating the cover legendary, so you are better equipped to wield the legendary in battle when it's all said and done (and even if you knock it out, if it does rear its head again, you can deal with it easier).
In the Devon Corporation building in Rustboro City, there's 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 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.
Also, since they're his family, of course their opinion of him would be favorably biased (unless they're a Dysfunctional Family, which they're not).
The remakes subvert this thanks to a bit of Show, Don't Tell. If you defeat the Winstrates, you can find Vito's grandmother polishing one of his several trophies, and his updated party implies that he's travelled to Unova for training. Vito might very well be one of the better NPC trainers... until he meets Brendan/May, whose role as the Player Character kicks him in the Poké Balls so hard, he retires from training from the loss. Vito basically represents the many other trainers of the Pokemon world who don't even get a fair chance at their dreams thanks to this being a franchise with many kid heroes.
Gardevoir's loyalty and devotion makes sense from an evolutionary (Darwinian that is) standpoint if you look at its 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 very vulnerable. And think about humans, they can't fly, shoot fire, or attack with their minds. Gardevoir sees its trainer as a defenseless child so the instinct carries over. The same can be said for Gallade, the Gen IV evolution, a chivalrous pokemon who also protects the weak.
Who happens to be the main trainer in Gen III to have a Gardevoir? Wally, the Ill Boy, easily one of the most vulnerable major characters in game. In the remakes, he had a Gallade, a Pokémon known for fighting fiercely when protecting someone.
Alternatively, when it's a much weaker Ralts or Kirlia, its trainer would be protecting it. Once it becomes a more powerful Gardevoir/Gallade, it can finally protect the trainer who protected it.
A meta example. In the games data, there are 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!
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?
Interestingly, the same can also be said of the anime, where, over 10 years ago, Blaziken was the first form of any Hoenn starter shown.
Blaziken's ability (Speed Boost) also makes sense when you think about this.
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.
For most people, "Omega Ruby" and "Alpha Sapphire" come across as weird titles, especially in the wording order, but this cause two bits of brilliance:
Their acronym, ORAS, has the Bilingual Bonus of being Lithuanian for weather, and it's also Filipino for 'Time'. The Alpha villains try to bring everything back to the beginning of time, and inadvertently bring about the end of time.
All life started at sea but ends up on land.
Two critical locations are Mt. Pyre (where the Orbs related to Groudon and Kyogre can be locates) and Cave of Origin (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 Primordial 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 its 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 its 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 its dreams.
Similarly, the fandom loved Salamence for being a badass western dragon whose secondary flying-type was overshadowed at best and considered a liability at worst even before power creep set in. Its mega evolution makes it incredibly dangerous not by making it a better dragon, but by making it a better flier.
Its Defense is equal to a Cloyster's. It's covered by a Shellder, Cloyster's pre-evolved form. The Shellder basically evolved (for the battle).
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. 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 Blissey. 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.
As stated in X and Y, Mega Gardevoir's chest plate (its heart) is in two pieces, representing it opening its heart to its trainer. When Gallade Mega Evolves, similar plates appear on its arms, meaning that Mega Gallade literally wears its heart on its sleeve.
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, none 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.
In the remakes at least you may be just a kid but you're one of the best, if not the best, trainers in the region. You defeated Magma/Aqua and saved the region. A little generator giving off a false alarm isn't a problem for the champ.
Okay, stuffing more than 30 legendaries in one set of games might be a tad overboard. But if you take into account that excluding 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 than 3 I Vs of 31 when generated in the wild, all of these legendaries are almost guaranteed to be competitively strong.
Also there's fact that the only non-event legendaries you cannot obtain are from Kalos and Kanto. Kalos is because this is G6 and there is no need to. But G1 is because Hoenn is contemporary with Kanto (at least in the original timeline), thus probably being caught by its protagonist. All other non-native legendaries (other than legendary beasts because of FRLG; though there could be more than one of these) are from future games, so it's okay - who's to say that the legendaries you have caught before haven't been caught by Hoenn protagonist before, but then got released in some way?
You may have noticed that most of these legendaries are found in dark portals with golden outlines. These are exactly like the rings on Hoopa (an unreleased Pokémon), and especially like the big ring on the body of its Unbound forme. Leaked event dialogue from X and Y reveals that stealing things into pocket dimensions — including an entire castle — is Hoopa's modus operandi, and it does this basically For the Evulz. Dropping a dozen Olympus Mons on Hoenn is Hoopa's idea of a joke...
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.
Besides, the player character moves from Johto to Hoenn in the beginning of the game - the Johto games do not involve character customation. However, their remakes do involve the character swapping outfits for plot reasons... Incidentally, this is also the case in RSE and ORAS, where RSE features no changes but ORAS has you change into special suits. Mythology Gag?
Also, in Pokémon X and Y and Pokémon Sun and Moon, you could justify the customization by arguing that the player character takes after their father. However, since you see both of the main character's parents on-screen in Hoenn, it would be a bit weird to give them, say, blonde or red hair, or much darker skin.
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!"/"Pfloosh!" (which sounds like water gushing when spoken aloud) and the Team Magma Poochyena say "Bufoh!"/"Pwamp!" (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. This doesn't just applies to the legendary, most Pokemon exclusive to Omega Ruby have red, brown or warm colors in their achemes, while those in Alpha Sapphire have different shades of blue, with a few exceptions having cool colors instead.
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.
And also perhaps the side games. Pokémon Mystery Dungeon is implied to be a world where humans existed at one point but were wiped out, existing only as fairy tales. Coincidently, in the first game there was also an unexplained meteor, that housed Deoxys, hurdling towards that world, that Rayquaza had to stop. Foreshadowing perhaps?
Apparently, Deoxys's psychic powers cannot overcome the force of gravity or the ground's friction, since in Birth Island the player has to push the triangle manually. In space however, the triangle solves itself.
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!
Latias and Latios's normal colors are red and blue respectively, obviously representing Ruby and Sapphire. But then, you also notice that, going by additive color, their shiny colors each add green (Emerald) — red + green = yellow, and blue + green = cyan!
While not necessarily connected to the colour of the games, Lunatone's shiny form is pretty clever — its blue eyes are a Stealth Pun of "once in a blue moon", which describes shinies rather accurately.
A lot of people complain that May is too busty for a kid her age. Ignoring the fact that it is possible for someone of ten years old to be that size, May's never said to be ten in the games. The only protagonist with an age is Red (and by connection, Leaf) who is eleven. May can be anywhere from eleven to thirteen for all we know. May is, however, explicitly ten in the anime, and not more than thirteen by her reappearance in DP according to Pokemon Anime timeline theory. So, if the anime mimicked the games, May was also ten in RSE.
In the anime, yes. Since the games came out first and are separate canons from the anime, it's fully possible for Game May to be slightly older than Anime May.
May will always be approximately 11 in the anime because time doesn't pass (which Word of God confirmed in a 2017 interview). As for the games, there have been cases where girls as young as nine have started puberty, so it could've applied to May, who is implied to be (and confirmed in ORAS) 12 years old. Note that most of the other females, from the 11-year old Selene, to the approximately 14-year old Hilda, don't have much in the breast development, and puberty can come as late as 16.
When one travels to Navel Rock, there is no mountain in the overworld, but Ho-Oh is on top of a huge mountain that you have to travel up 10 or so ladders to get to. This seems weird at first, until you realize you first enter the chamber, then go down a ladder, and then walk down an extremely long hallway. The mountain that Ho-Oh is on top of is a long way behind Navel Rock, you just can't see it.
Where do you first find wild Absol in the GBA or 3DS games? On the routes between Fortree, Lilycove, and Mt. Pyre. When does that happen in terms of story? When Magma/Aqua are about to steal the Blue/Red Orb to reawaken Groudon/Kyogre and Dry out/Flood the earth. The Absol are trying to warn the player! Which makes it all the much more satisfying to capture an Absol, level it up, and use it to stop them.
In real life, there's a common meteor shower that happens every so often called the Leonid Meteor Shower, named in association with the constellation, Leo the Lion. What is it called in ORAS? The Litleonid Meteor Shower.
Kyogre is about 15ft tall and its appearance heavily resembles a killer whale. In its Primal Form, it grows to about 32ft tall. The largest male killer whale on record was 32ft tall.
The sea covers about 70% of the earth, which makes it more than twice the size of the land. Primal Groudon is about 16ft tall. Now with all this in mind: what is 16 times 2, again?
Zinnia talks about the existence of the original game's reality and asks the player what would happen if the meteorite that was heading towards the planet were to collide with it. Said meteorite was mentioned to be heading towards south of Sootopolis (where the other secret/post-game islands of Hoenn were in the original games) and contained Deoxys within it, complete with the same triangle with it inside that appeared on Birth Island. Piece these facts together, and you'd realize that said event did, in fact, already happen in the original game's continuity, with the result being that said meteorite became Birth Island and that nothing else was effected.
If you look closely on the base (non primal reversion) forms of Groudon and Kyogre, you see that they already had the Omega symbol and the Alpha symbol on them. In other words, they had the "Alpha and Omega" symbolization since they were introduced, thus explaining why the remakes are called "Omega Ruby" and "Alpha Sapphire" in the first place.
A random man in the Battle Resort literally speaks Japanese if you were to talk to him within the English version of the game. This, in spite of the fact that Hoenn is analogue to one of the islands of Japan. This may seem confusing at first, until you realize Translation Convention could be in effect here, especially once you've encounter an NPC from Unova on SS Tidal that claims to struggle speaking your language. (Indeed, his speech is depicted in a "You No Take Candle" manner.)
Going to the Mossdeep Space Center's control room after the Delta Episode reveals a bonus cutscene where the scientists managed find out that Deoxys was on the meteor that was heading towards Hoenn and had merged with said meteor at some point during its life. The scientist also theorized that Deoxys wasn't really intending on destroying Hoenn. Rather, it was intending to come and visit the planet. While the scientist was left wondering why it wanted to do so, it's easy to guess that it got curious at the planet that gave it its current form and wanted to see the planet for itself. As a last-ditch effort due to its point of entry being ruined, Deoxys attacked the player in an attempt to get itself captured just so that it can still get to see said world for itself.
This makes even more sense when you remember that the original R/S/E games are alternate reality versions of the remake's timeline. In the originals, you never encounter Deoxys in space, yet there's never the impending doom of a meteor crash, and instead you find Deoxys and the same triangle that appeared in the meteor on Birth Island. The truth is the earth was never in danger, since Deoxys itself would've somehow stopped or destroyed the meteor once it reached the Earth. Basically in the remakes you and Mega Rayquaza blow up Deoxys's space sedan. Nice Job Breaking It, Hero!.
In the Battle Resort, there are trainers who specialize in Grass, Poison, Fairy, Ground, and Bug-types. These are the only types not used by any Gym Leader, Elite Four member, or Champion (Steven counts as Steel) in Hoenn.
The energy that is related to Mega-Evoution is called Infinity Energy right? While Groudon and Kyogre had Primal Reversions, Rayquaza has a Mega-Evolution instead. If you look at Rayquaza, the Tron Lines/Streamer patterns incorporate Lemniscates, or sideways 8s. What is a Lemniscate the symbol of? Infinity.
Valerie from X and Y mentions that she's fascinated with the concept of becoming a Pokemon and that her fashion style has been influenced by that. Her winged dress didn't exactly resemble any Fairy-type Pokemon...until these games introduced the Normal/Fairy Mega Audino, who sports similar wing-like frills that are nearly located in the same places on its body as are those on Valerie's outfit.
Take the initials which tend to refer to the Hoenn games' names - R, S, E, OR, AS. The games where team Aqua appear spell out SEAS, and taking the games Team Magma appear in spell out ORRE... The setting of Pokémon Colosseum and Pokémon XD: Gale of Darkness, which just happens to be a large desert and also is where the player gets to battle robots based on Kyogre and Groudon.
Some gyms in Pokemon games (especially in Unova) are themed after other types of establishments—for example, the Rustboro gym in Hoenn is a museum, the Striaton gym in Unova is a restaurant, and the Lumiose Gym in Kalos is the Eiffel Tower. Brawly's gym is one of these too, and it's a...
Brawly's dialogue tends to be somewhat awkwardly written in ORAS especially, what with things like "surf your giant wave". Then a TV show in-game confirms that Brawly is originally from Kanto. Suddenly it makes sense - even ifCommon Tongue is in play, what could sound perfectly natural in Kanto-dialect might come across as odd in other regions, and you never meet him on his "home field".
Courtney's new hair style and color in the remakes is very similar to that of the female Psychics in the original games, who are no longer present in the remakes. It might just be a case of a visual equivalent of a One Steve Limit.
In Pokemon Generations episode "The Vision", Courtney has a vision of a possible future, usually a power Psychics have.
Team Magma and Team Aqua share their initials with their respective leader's name. The leader of Team Magma is Maxie, while the leader of Aqua is Archie. Seems that both of them had a small bit of ego in their naming schemes.
This holds true in almost all official translations that make use of dub name changes - even the Korean, which otherwise has pretty odd translation choices at timesnote just as an example, they typically keep the tree-theme among professors, but apparently decided just to name Birch a slang word for "exceptionally hairy people, particularly men" anyway. The exception being Chinese, where 'Maxie' and 'Magma' don't share any syllables at all... But 'Archie' and 'Aqua' still share the same symbol. Consider who is the more boisterous of the two, and it makes sense that it wouldn't be the other way around.
Banette's Ghost typing makes a lot of sense when you consider that it's a child's old doll that was thrown away and empowered by vengeance. Children usually treat their toys like they're alive, giving them personalities and whatnot. Throwing it away is the same as killing it, so it's a ghost looking for its murderer. In fact, you could even say that Shuppet is the original "spirit" of the doll, and it becomes Banette by the emotions growing strong enough to (re)animate the doll, making Banette essentially a zombie.
Zinnia's Pokemon is named Aster. Aster and Zinnias are both flowers. Additionally, their names start with the first (Alpha) and last (Omega) letters of the English alphabet. They're also Draconids (Delta).
Also, they weren't around at the time of the original games, only in the remakes, and they were introduced in Gen VI, the same generation whose main games have a character called A.Z. who is also related to a flower, or rather a Floette.
How does Rayquaza Mega Evolve without a Mega Stone? It doesn't. It ate the Meteorite, which has the Mega Evolution symbol on it. Its Mega Stone is internal.
Early in the game there are two rich trainers who both use a full restore during battle. At first glance, the explanation seems to be they're rich enough to afford full restores this early, but that falls flat when you consider the items that can be bought depend on where you are, and we're nowhere near where you can purchase them. The real reason? Consider they both have Zigzagoon. They got them via pickup, which, in Ruby and Sapphire, have a 10% chance at getting a full restore. This ceases to be true in Emerald and the remakes, however: from Emerald onward, what you can get is tied to the Pokemon's level, so you can't get full restores until level 21 at earliest, and even then the chance is only 1%.
The Sealed Chamber in Generation III, where you unseal the Regis, says "We sealed the Pokémon away. We feared it." Why would three Pokémon be referred to collectively as "it?" Then Generation IV brought us Regigigas, and you need the three golems from Gen III to wake it up - the Sealed Chamber was using the word "Pokémon" in the singular, not the plural, and the "it" is Regigigas, who they sealed away using the other golems. Ergo, a seemingly nonsensical sentence in Generation III was actually foreshadowing the appearance of a new legendary in Generation IV.
The idea of berries was greatly expanded upon in Generation III, with 43 berries in Ruby/Sapphire compared to 10 in GSC and NONE in the originals. Clearly, the soil of Hoenn is far more fertile than in any previous region. Bring in Team Magma, with the blazing sun caused by Groudon; and Team Aqua, with constant rainfall from Kyogre. Plants need both sunlight and water to survive, but having too much of one, with little of the other, will probably kill plants or stunt their growth. Furthermore, in Emerald, these two extremes of rain and shine alternate instead, making the weather unnatural. While it could also destroy plant life (although some plants can live with it), it also has a more noticeable effect on animals and even humans, like your allergies acting up. Not to mention, one of the two warring Pokémon will have to win eventually anyway. Realizing that Hoenn's way of life is clearly centered around its climate and crops, Team Magma and Team Aqua may actually be the most devastating villain team of any Pokémon game.
Beldum is only able to learn Take Down. This makes sense as, without merging with another Beldum to form a Metang, it's body and mind wouldn't be complex enough for either it's psychic abilities or any moves more complex than slamming it's entire body at somebody.
In the remakes, each member of the Elite Four has an elaborate pavilion and when you get close to it, there's a cutscene where the pavilion's outside comes to life. Sidney, the Dark-type Elite Four member, has a pavilion surrounded by sand, and his cutscene shows the desert lighting up. It seems more appropriate for a Ground-type user... until you remember that the Dark-type is all about deception and trickery. He's trying to trick challengers who didn't do the research into thinking that he uses an entirely different type.
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.
Groudon's ability working underwater veers right into Fridge Horror if you think about it from a physics standpoint. A sufficient source of heat can flash-vaporize water. To do it underwater, you'd need a massive amount of heat, for example a nuclear bomb, like the one in Pacific Rim for instance. You're walking around with something producing as much heat as a thermo-nuclear explosion near-constantly. Convection Schmonvection is clearly in play with Primal Groudon. On the other hand, by the time you encounter Groudon, you have the Blue Orb which is supposed to counteract Primal Groudon's magic.
More generally - there are no restrictions at all on what Pokemon or attacks you can use while underwater, which takes the old conundrum of how Golem can be used while surfing Up to Eleven. Lava snails can survive and breathe fire at the bottom of the ocean; electric attacks can be used without electrocuting the player character. At least in ORAS the player is given a scuba mask when they get dive. Though that still doesn't explain any non-Water-Types they may have...
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. And even more baffling, you can use Primal Groudon, the second heaviest Pokemon in existence, with no consequences.
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?
Once you rescue Professor Cozmo, your rival asks if you'd like to go back to Mauville City with them, and says that they intend to get their next badge from the Mauville Gym. Since you can't get past the boulders blocking Route 111 without Rock Smash, which you can't use unless you have the Mauville Gym Badge, how did your rival get past the boulders?
Starting in this generation, the games add a little blurb whenever you lose a fight. After blacking/whiting out, the player "scurries back to the Pokémon Center," while somehow preventing themselves from being attacked. How? It sounds like the user has some sort of medical condition that means they shouldn't be training Pokémon in the first place, because blacking out is another way of saying fainting and whiting out is usually caused by hypoxianote low blood oxygen levels and typically is followed by passing out. Even if they don't, the lack of oxygen means they'll probably be dizzy and unable to walk properly. It seems like they added the message to explain away some existing Fridge Logic (i.e., how they got to the Center in the first place), but it just opens up more questions.
In medicine, a "blackout" is a form of amnesia which may be caused by a recent traumatic event and/or stress — such as, say, losing a battle — in which case one may forget everything that happened right before or right after the event, known as anterograde amnesia. Sounds familiar, huh?
Chaz becoming Brawly's student, while a fun character moment, raises the question of how the two got to know each other, given that Chaz hasn't yet started challenging Gyms and doesn't have any connection to Dewford Town that we know about. While it's totally possible that Chaz simply approached the Fighting-type Gym Leader apropos of nothing to help him out with his Fighting-type Pokemon, and Brawly went with it, it's also wholly possible that Lisia introduced the two of them. Brawly is said to be friends with Steven, who in turn is close friends with Wallace, Lisia's uncle: it's likely that all three of them know each fairly well, which would give Lisia the connection necessary to ask Brawly to mentor her "rival."
This seems more like Fridge Brilliance than Fridge Logic since there's a logical explanation there. That aside, though, considering that all of the gym signs have what types the leaders train on them, the fact that Brawly specializes in Fighting-types is probably common knowledge. It's really not that weird that Chaz would want to ask for advice for his Machoke from a Fighting specialist.
After Groudon/Kyogre is awakened a certain weather effect takes place in the respective game that stays up 24/7 until you defeated or caught it. Kyogre's super-storm would be terrifying enough but Groudon's weather is harsh sunlight. The Fridge Horror? Groudon is powerful enough to tidally lock the planet, and with Hoenn sunny side up!
At the end of the Sky Pillar climb during Delta Episode, Zinnia says that the reason she went to the extremes of stealing Key Stones was because she didn't want to risk not doing right by "those who could not... live up to that fate". And when she prepares to begin the ritual to summon Rayquaza, it's clear that she's preparing for not surviving it, and it's pretty clearly straining on her. Earlier on, when you meet Zinnia's grandmother, and she says that the Draconids' reversals of the last two disasters both required a good deal of sacrifice, and Zinnia's willing to let the "sacrificial blade" aim at her own heart. How many Draconids died in previous summoning attempts for the third go-round? And even worse: is that what happened to the first Aster?
It gets worse. Even if she did survive summoning Rayquaza and managed to bring it under her command, the next step would have been riding it into space to destroy the Meteorite. But Zinnia doesn't have the suit the player got from the enemy team, so she'd have nothing to protect her from the vacuum of space. In other words, while summoning Rayquaza had a definite possibility of dying as a result, riding Rayquaza to destroy the meteorite without any kind of protection would definitely have killed her.
There's one silver lining, though: Mega Rayquaza seems to have no trouble at all being in outer space. You could Hand Wave it as Rayquaza being a legendary if not for the fact that it seems to be projecting its Delta Stream ability around it and the protagonist... Also, Zinnia initially attempted to summon Rayquaza by helping Team Magma/Aqua. If everything had gone "correctly" there, then Zinnia may have been able to get her hands on the Magma/Aqua Suit that way.
The notes at Sea Mauville pretty much confirm that this has happened at least in the past, to our horror. In one of the cupboards, there is even an energy drink made of "Seviper Extract"... It's implied that this is why Wattson put a stop to the New Mauville project, as the nature of the energy extraction was too gruesome for him.
The truth of the matter is revealed if you talk to Wattson and his wife after checking on the possible malfunction in New Mauville. Namely, the completion and utilization of a 69-floor underground city would have been detrimental to the local wildlife. However, the Seviper Extract is unnerving in a different fashion. If you translate it to real-life terms, you get...snake oil. Mauville Holdings was giving its employees mere placebos.
How could Mewtwo have any Mega Stones when the Kalosian War occurred millenia before it was even created? We might have to thank Maxie/Archie for that. That skyward burst of Infinity Energy that came from the Cave of Origin when Groudon/Kyogre was taken care of happened to create a new batch of Mega Stones when the leftover energy rained back down, and the Hoenn and Kanto games take place around the same time.