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.
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.
On that note, who happens to be the main trainer in Gen 3 to have a Gardevoir, but Wally, the Ill Boy, easily one of the most vulnerable major characters in game.
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?
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.
Also, 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.
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.
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 betweenthetwo. 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 plumageit 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.
I kept wondering what the point of making Mega Audino was. It looks so much like Audino's Blissey equivalent I couldn't figure out why they didn't wait until next gen to include it as a regular evolution. Then I remembered 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.
The player witnesses Wally capturing a Ralts as his first Pokémon with Norman's Zigzagoon. We then see Wally give the Zigzagoon back. The Ralts, however, is at such a low level that it doesn't know any damaging moves yet. How is Wally supposed to level up his Pokémon if he can't have it fight or use it to catch other Pokémon to help gain experience?
Com Mons tend to be easy to catch even if you don't weaken them first. Perhaps he just kept tossing Poké Balls until one finally worked, and then used that Pokémon to help him level up his Ralts.
Or, he just used a Rare Candy, to get his Ralts to Level 6... boom, Confusion.
Wally moved to the town right next to the daycare center. He probably left his Ralts there for a couple levels.
Related to the above: We see Norman give Wally a Zigzagoon when Wally goes to catch Ralts. Wally returns it. In Ruby and Sapphire, Norman does not have a Linoone, so what happened to the Zigzagoon? This may be part of the reason why he was given a Linoone in Emerald, but wouldn't Norman giving Wally a Slakoth make more sense?
Most players will have dozens more Pokemon than they use in their 6 slot limit. Perhaps that Zigzagoon was just one he caught or a baby from others in storage.
It has been heavily hinted Gym leaders have multiple teams. Perhaps for trainers who come from Rustboro for a first or second gym battle (Who are not the leaders son or daughter) fight a Slakoth and Zigzagoon.
Actually, Norman has a Linoone in Emerald.
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.
Sunny Day and Sandstorm make even less sense underwater.
On the contrary; Drizzle doesn't need to be rain water. You're in the ocean. Water attacks boosted from the water you're in. Sunny Day? Light is amplified in water. Sandstorm? You're in the ocean, the ground is all sand. Kick up a bunch of sand, and you have a sandstorm.
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.
Were this 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.
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?
On the other hand, especially if you are not a metagaming player, the fact that Wally managed to make it so far and do so well against you belongs to another page.