One may think of Red as overpowered, due to him catching all of the Pokemon and beating the Gym Leaders with ease. Then you remember, Red getting all of these things is just like how anyone would play the Pokemon games!
Despite the eventual Dub Name Change, Blue/Green can afford to retain his green shirt as its color, together with his purple pants, as both are analogous to blue.
Not only that, it reaffirms his reasoning for choosing his starter—he wouldn't pick Bulbasaur or Squirtle for his name sake, then ultimately picks Squirtle for the type advantage.
Shout out to the American fans - while Red selects Charmander, the unevolved mascot of Pokémon Red, Green picks Squirtle, the unevolved mascot of Pokémon Blue, with both games being the English paired versions.
Blue holds off on letting his Squirtle evolve into a Wartortle, as demonstrated by using Bite during his first battle with Red; this tactic hints at the fact that Blue actually has some knowledge of raising Pokémon effectively.
Not only that, Red's Charmander had just learned Ember, the very first Fire-type move it would learn in the game. That means that Blue's Squirtle was Level 22 while Red's Charmander was... level 8-9. Blue's Squirtle was as strong as his starter would be when you get to Cerulean City, just two times stronger than Charmander was.
Blue's Squirtle being overleveled may be a reference to some players over-grinding their party before even reaching the first gym.
The English Dub's version of Charmander's infamous scream is both this and Fridge Horror at the same time. Some people have complained about the scream being toned down to mere struggling and grunting... until you realize that Squirtle was biting down on Charmander's neck (or at least started at the side of the its face and then moved down to the neck for a more effective grip); it was losing air to breathe, so obviously its scream couldn't last long and was now just struggling to not die of asphyxiation.
Even if Rhyhorn is a much higher level than Red's Jolteon, how could Rhyhorn's Thunderbolt be able to One-Hit KO it despite the fact that it has the ability Volt Absorb (which turns Electric-type attacks into an HP bonus)? As an adaptation of the original games, Jolteon didn't have Volt Absorb at the time.
This scene is intentionally exaggerated, with it being lampshaded by Red and Giovanni to highlight Rhyhorn's power further. As long as it can damage Jolteon, defeating it is possible.
Another possible (and more likely) explanation as to why Thunderbolt hit, instead of just not having an ability, Red's Jolteon might have had its Hidden Ability instead, Quick Feet.
Alternately, abilities were implemented into the games in Gen 3. This is somewhat contradictory to the existence of Mega Evolutions, but it is possible that abilities don't exist in this canon.
Why is Charizard the most powerful Pokémon on Red's team? Because like most kids Red probably went through most of the game just with his starter.
Some have complained about how Red had caught a Spearow at one point, yet is later shown capturing a Fearow, and thus seeming a bit like a hypocrite. However, when one recalls that in game, you can trade a Spearow for a Farfetch'd... that's probably what happened.
This adds extra brilliance to the games: when Red goes to challenge Brock, Brock first asks Red how many badges he has and then chooses weaker pokemon to battle with in according to Red not having any badges. This explains why, in the games, whenever you re-challenge a gym leader they're stronger and even potentially have new pokemon from different regions.
During the same battle, a spectator quips "It's not very effective..." when Charmander uses scratch on a Geodude—a perfect explanation for those dialogue boxes that occur during battles!
In the Elite Four battle, Dodrio tries to attack Gengar only to phase right through its body. Dodrio was most likely using a Normal-type move there, which are ineffective against Ghost-types.
The Ground-type Marowak dies to an electric strike, something that she should have been unaffected by (as Ground-type Pokémon are themselves immune to Electric-type attacks).
One could argue that it died of blunt force trauma, either way, it's still pretty horrific. Though that itself raises the question of how you inflict blunt force trauma on a creature with an armored helmet (possibly by attacking below the helmet or really even shocking below the helmet, because the body doesn't really seem to be dirtish except for the color).
There's also the fact that the Cubone was already wearing a helmet (which in the games is said to be the skull of its mother) before said mother is killed. Granted, they probably wouldn't have shown either a helmetless Cubone or the procuring of its helmet, for obvious reasons, but one has to wonder where it got the skull helmet from.
Additionally, it could be a different kind of electric strike than that of an Electric-type attack (if Ground-type Pokémon can Surf just fine without injury, one can probably assume Pokémon attacks don't function exactly the same as real elements). After all, if there were inventions made to attack Pokémon, there would probably at least be precautions put in place to make sure it didn't just not work against an entire type.
The written text in the special is shown to be in a fake script. Which wouldn't be so bad, if it weren't for the fact that if Pokémon Gold and Silver were to be adapted as well, they need to figure out why the Unown looks like letters from the Latin alphabet instead of the glyphs from whatever script the world's text is in.
Just because the faked script is not Latin doesn't mean that Latin alphabet doesn't exist. There are many languages in the real world that are not based on the Latin alphabet, and considering that many Pokémon regions like Kanto, Johto, Honen and Sinnoh are based on real-life regions in Japan, it was not really a problem to began with.
Blue mentions that, had he captured Mewtwo, his Pokédex would have been completed. However, wouldn't that imply that he had captured all of the Legendary Bird Pokémon as well, despite Red already taking Articuno, Moltres, and Zapdos? This would differ from the games, where there is only one of each.
Notably, Blue's mission is combat, not capture. It's entirely possible that Blue sees 150 Pokédex entries as "seen and fought" (akin to later games), in contrast with Red's "caught and analyzed" (akin to Gen I).