Why did Pikachu and Red not visit Alola during their travels as a sort of teaser for it? Because they encountered Zygarde's Complete Form, which is a Gen 6 Pokemon whose form debuted in Gen 7.
It may have also been meant as foreshadowing for his appearance in Sun and Moon.
Pikachu failing to defeat the Wooper in the Johto region seems to have been intended to show how much Pikachu is improving by comparison in the next few regions. However, it actually does make sense when you remember their respective types - Wooper's part Ground-type - hence it being unaffected by Electric attacks.
Also they'd be the very first Water/Ground types seen in their travels, meaning that they'd be completely blindsided by such a combination existing.
As described by Bulbapedia, Volt Tackle in Generations makes Pikachu appear to be black and white. Pikachu also was shown using this move in Relic Castle, Unova.
The ending of Episode 2 does this for Pokémon Gold and Silver and its remake Pokemon Heart Gold And Soul Silver, by claiming that Giovanni's disbandment of Team Rocket was actually a lie to rebuild in secret. This would explain why Giovanni never showed up in Gold and Silver, because he isn't going to blow his cover three years down the line.
Looker being present as a Global Police Agent in Episode 2 seems to simply be due to popularity, until you remember that in Red/Blue/Yellow you encounter a Gentleman on the S.S. Anne who claims to be a Global Police Agent on the trail of Team Rocket◊. Could that have been Looker in one of his disguises?
Magnemite was the only Grunt Pokemon who was left standing after being hit by Dragonite. This may be a reference to how Sturdy Pokemon can hold on from one hit knockouts after Generation 5.
If abilities are in effect, Houndoom being KO'd by Flamethrower makes sense. Team Rocket - as a criminal organization - probably does a lot of their crimes at night, where a lot of Pokemon with sleep-inducing attacks are about, like Gastly, Oddish, and Hoothoot. Having an Early Bird Houndoom would be useful at that time instead of Flash Fire, given that Fire-types are somewhat scarce in comparison.
Dragonite just shrugging off Team Rocket's attacks may mean that Team Rocket's Pokémon are really weak, or that Dragonite is really strong... But what if Lance's Dragonite was actually using Barrier?
Unlikely, as Barrier only raises Defense and Dragonite was hit with special attacks. However, it was glowing white for a second before getting hit, so it's possible that it used Protect or some other move.
Courtney's vision in Episode 7: was that the future, or was she just seeing things? She's always had a reputation for having a vague mental disorder, but perhaps it is even more than we assumed. But, if anyone remembers what the RSE Psychic trainer sprite looked like back in Gen 3, then her apparent precognition may make more sense. Namely, that was her original Trainer class, before joining Team Magma.
Many have wondered why Blue/Green's ace Pokémon was Blastoise, despite Red being shown using a Bulbasaur before capturing Pikachu? Red had three Pokemon in his Pokedex registered before fighting Pikachu, and as it was a Gen 1 intro screen shown that means captured, not seen. Red had already obtained three starters (somehow) by this point, but he likely started with Charmander, hence Blastoise. Also he was using Bulbasaur because it could take a Thundershock stronger than the other starters, and also as a part poison-type it would not be poisoned by Viridian's swarms of Weedle.
Why did we not see any Gen 4 protagonists? Because, in theory, the next generations to get a remake is Gen 4. As the previous set of protagonists used their new designs, using the old ones for them would rapidly date Generations.
Replacing the Gen 5 Protagonist's role in the battle at Plasma Castle with Iris isn't just a case of trying to unite both Black and White's roster of Gym Leaders. Her title is The Girl Who Knows the Hearts of Dragons, and what types are the titular legends?
Why does N have Reshiram in this version? After all, most adaptations, including Pokemon Adventures, give him Zekrom, with the main exception being the Pokemon anime after Zekrom ended up being tied to Ash via earlier appearances/making it unable to be sealed and revived. It's because that this series was made for Western audiences primarily, where most players played White. Thus, N revived Reshiram, and the player character got Zekrom.
Possibly doubling as Fridge Horror; why would Chansey be afraid of the old chateau's Ghost-types when she, as a Normal-type, is unaffected by them? Because it works both ways. Chansey's Normal-type won't do anything to a Ghost-type, so she would be unable to protect her Trainer.
When Cheryl first appears in the game, she asks the protagonist to escort her through the Eterna Forest because she's afraid of being attacked by members of Team Galactic. If Episode 10 is meant to take place before this, then it does a good job of explaining exactly why she's so afraid of being alone in the forest.
The most commonly seen character in Generations is Looker, suggesting that he could be considered the closest thing to a main character. This could be oddly true, but he's also the human character whose appeared the most times in the games in the franchise (appearing in Platinum, BW, XY, ORAS, and SM). Of course he'd appear in this series the most.
There are ongoing themes set in the regions:
Kanto has a theme of updating for the audience: Red taking Ash's role as a region explorer with a Pikachu, the mascot for the entire Pokémon franchise. It also has a theme of accomplishments: Pikachu and the Gen 1 trainer traveling across the regions doing great things and meeting many Legendaries like Landorus, Regigigas, and Zygarde, then Blue becoming the Pokemon champion before Red does the same and ending with Giovanni making his escape from the International Police without a scratch and getting Team Rocket underground, keeping it intact until the Johto games. This can relate to the series's 20th anniversary and what all of the various fans of the franchise have done.
Johto has a theme of legacy, given that the episodes focus on Team Rocket's return, Silver's past, and the origins of the Legendary Beasts. It is fitting for a region with rich lore and rustic feels, and is also the setting of the first sequel games.
Hoenn has a theme of punishment: both Teams Magma and Aqua messed with Groudon, Kyogre, and nature and got messed up in return. Meanwhile, Gabby and Ty look at confidential information at the Mossdeep Space Center just to get a story and run into trouble because the scientists don't want people to know about extraterrestrial Pokemon.
Sinnoh has the theme of fearsome entities: the ghosts, Giratina, and Heatran relate to the stronger ties to the in-universe religion and mythology of Sinnoh and help build up how powerful these creatures and deities are.
Unova has the theme of story, owing to the fact that Gen 5 is the most story-driven generation and how the shorts in Gen 5 are much more tied together than those of the other regions.
Kalos has a theme of tragedy: Lysandre's Start of Darkness (becoming the leader of Team Flare and repairing the ultimate weapon), Looker's friend Emma gets hurt while disguised as Essentia, and finally, AZ recounting the events of the Great war and his guilt for his misdeeds. However, the scene of the Eternal Flower Floette returning to AZ at the end is a moral that tragedies are quicker moments and people can still be happy afterwards.
The flashback to the war 3,000 years ago had Magneton and Magnemite in it, but no Magnezone. It is an odd choice of Pokémon, but Magnezone evolves because of special magnetic fields that do not occur naturally in Kalos. They evolve only around the artificial Kalos Power Plant, which of course did not exist 3,000 years ago, nor did any similar locations as far as we know.
How was Zekrom able to match the power of a fused pair of Tao dragons? Simple, compare the two trainers, whose more likely to have battle trained between the trainer and the medium?
Arcanine burned a hole through the wall of Viridian Gym so hot, that it melted. Yeah, good thing no one was at the end of that attack.
Episode 4 had a moment where Lance's Dragonite knocked all of Team Rocket's Pokémon off a bridge over a very deep pit.
Episode 8 takes pains to show Water Pokemon suffering, putting to rest any idea of at least them surviving Kyogre's wrath, as opposed to the more immediately obvious one that Groudon would do.
Episode 10. Just, episode 10. For one thing, does this take place before or after we meet Cheryl in game? if after......
Episode 10 also casts the Ghost Pokémon from the main anime and their illusion powers in a much more disturbing light. Forget chasing people and Pokémon around with images of obvious fears or logical weaknesses. This is what they'd be capable of if they really had it in for someone.
Arcanine burning a hole to get inside was pretty cool to see, but what exactly would it accomplish? It would be too hot to immediately go through the newly created entry.
A way to break through walls that can't be punched through perhaps?
Or perhaps it was less about getting inside, and more about making sure any Team Rocket grunts inside couldn't get out that way- Hard to use a corridor that's filled with molten metal, after all.
What was the point of both Arcanine and Machamp busting through the walls when Magnemite just scrambled the electronic lock?
Attacking from multiple angles and locations is a common tactic.
For that matter, so it going through walls. Doors are usually covered by the enemy.
To not set off any alarms?
So wait... Literally no one knew that the identity of the Viridian gym leader is Giovanni? Did he forge his name when registering to be a gym leader or something?
"Oh, the Crime Lord is named Smith huh? And the Gym Leader is named Smith too.....weird how that goes."
Is it that hard to believe? He's got tons of money, power, and influence. It's all about giving the right people enough to keep them quiet ("Got a sick relative and high medical payments? Here, I'll cover them in full, as long as you..." etc.), or making them fear him more than they fear the authorities. Also, it's easy to miss, but in the games, the Kanto League only got started very recently by the time that Red set out on his adventure. There's an email in Oak's lab, from the League, announcing that they are "finally ready to take on all comers." That's probably also why there is no Champion when Blue battles the Elite Four (in the games, after beating Lance, he tells us that we/Red would have been crowned the Champion right then and there if not for Blue having just beaten him moments earlier). So Giovanni probably hasn't been a Gym Leader for very long, either - Blue and Red are likely among the first to even battle him as a Gym Leader.
(Original poster) Except the third short shows this detail has been retconned out of existence; Agatha says something along the lines of "It's been a while since a trainer has collected all 8 gym badges". Obviously, there has been another trainer who has who gone through all the gyms and won, including Giovanni's, and quite some time ago too, if "a while" is any indication. Then again, it's always possible that the previous gym leader stepped down; but still, I would understand if they didn't know the Rocket Boss's name or what he looked like, but the police clearly know both. The league at least would have profiles on their leaders, this isn't like Pokemon Go, not just anybody can be a gym leader and I can imagine there has to be a bunch of paperwork involved. Or am I thinking too deeply into this?
If you remember in the games, the Kanto Elite Four are also the Johto league's Elite Four. Agatha could be referencing Johto trainers that have beaten them. Also, Giovanni was never really around his gym, which looks pretty plain and barren. He could have been just running it as a side project/hobby with a pseudonym and have an underling occasionally act as the leader when audited by the league or whatever. There are plenty of real life examples of businesses with legit paperwork, but were actually money laundering schemes for crime rings. Plus, it's not like everyone in Viridian is going around talking about their famous gym and its glorious leader Giovanni, so it's kind of implied that the gym is just kind of a strange quiet afterthought in town. But yeah, in the end it is just a promo fanservice short for an all ages video game.
It might just be me, but I don't recall anyone knowing the name of the Viridian leader. Since he was a rich and powerful criminal leader, he most likely used a fake name for the official documents, and just didn't tell his name to the opponents he defeated, and since only Red had previous encounter with him, none of them realized who he was. Agatha's line might as well say that no one won eight badges since Giovanni took over, him being too strong for any opponent. Even if the police had known Giovanni's name and appearance from the beginning, they didn't know the Viridian gym leader's (also, in the game it was implied that the gym was used as a cover and a place to go back and rest a bit, so he likely got it before team Rocket became big).
So you're telling me, Looker washed up on the shores of Hoenn, got amnesia, was immediately summoned afterwards to conduct an investigation on Team Rocket in Kanto, spent some three years in Johto looking for Giovanni, and was then immediately called to Sinnoh to investigate Galactic there. Not only does this make generation III and I existing at the same time on the timeline impossible, there's no cool down time in between. Is... Is Looker the only Interpol agent there is? Are there many Lookers running around? Plotholes! Plotholes everywhere!
It is implied the Hoenn and Johto games take place a brief while (like, a few months) before the Kanto and Sinnoh ones, respectively. Also, running multiple investigations simultaneously really isn't impossible, and considering this is a world where psychic critters can be found around every corner, recovering from amnesia quickly couldn't have been THAT impossible.
There are a few possible options: either Looker washed up in Hoenn with amnesia after investigating Team Rocket in Kanto, then spent some time recovering during the three year gap between Kanto/Hoenn and Johto/Sinnoh; or this is an alternate universe to the events of Omega Ruby and Alpha Sapphire, since the possibility of alternate universes in the Pokémon world was discussed by Zinnia during the Delta Episode and implied to be the reason why the previous generations do not feature mega evolution (however this option is probably unlikely since Primal Groudon/Kyogre are on the poster artwork). Alternatively, the official timeline we've been given of the games simply shows their placement in relation to each other (e.g. Kanto and Hoenn being three years before Johto and Sinnoh), meaning the events of the Kanto and Hoenn games could be a few weeks apart from each other while still being considered timeline-wise as happening 'at the same time'; the beginning of Diamond and Pearl is a good example of this, since the broadcast about the Red Gyaradosan event that happens about halfway through the Gen 2 protagonist's journeyis being shown before Dawn/Lucas even obtain their Pokémon, hence the trainers of each game don't start and end their journeys at the exact same time. So, Looker may have had a few weeks between investigating Giovanni and somehow ending up in Hoenn with amnesia.
It's also entirely possible that Team Rocket caught on to Looker's investigation and took some mob-like street justice to the cop, giving him amnesia and dumping him in the ocean near Hoenn. Cue Brendan/May finding him at the Battle Resort, while still allowing "The Legacy" to take place three years later.
Regarding Looker's amnesia, certain plot elements introduced in Sun and Moon's postgame suggest that there's two Lookers. The Looker with amnesia is the Looker from the original, non-Mega Evolution, timeline, having been displaced into the Mega Evo timeline. The Looker who we follow in Generations is the one native to the Mega Evo timeline, who never had amnesia to begin with.