These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
The Marowak ghost isn't trying to attack humans; it's trying to warn people away from Team Rocket.
Giovanni. As a child he was a Pokemon trainer much like Red. When he battles Red, he remembers how much he enjoyed Pokemon when he was younger, making him something of an Audience Surrogate for older Pokemon fans.
Mewtwo is little more than an uncontrollable and incredibly powerful wild animal, which is a far cry from his portrayal in other adaptations. Consistent with those adaptations, he obviously wants to be left alone, but Red won't leave. On the other hand, this is basically how he was portrayed in the game itself.
Author's Saving Throw: The entire existence of Origins can be seen as one for Pokemon fans who wish the anime followed the games more closely. Its Darker and Edgier tendencies also are intended to appeal to fans of the original games who had outgrown the anime.
Mega Charizard X's reveal in this special. When Mega Charizard Y was originally revealed, it was said to retain its typing and was thought to be the final nail in the coffin for Charizard ever being a Dragon-type. Cue this special being aired in Japan, revealing in a post-credits sequence that Mega Charizard X was a Fire/Dragon.
Awesome Ego: Blue is every bit as rude and arrogant as he is in the games, but no less popular for it.
Awesome Music: Many of the classic themes from Red and Green/Blue are redone as proper orchestral pieces here. And it is awesome.
Although opinions of Origins' quality in general have been all over the place, it has been well-received overall with the fanbase due to the absence of many commonly complained-about elements from the main anime series. As such, it's almost universally considered better than most of the main anime; however, its quality compared to the earlier, Shudo-influenced seasons and movies is more debatable, especially if the original Japanese versions are being compared.
The reaction to Mega Charizard X debuting in the special. With the exception of the Mega Stone subplot (which is barely touched on until Episode 4), the OVA was very faithful to Red and Green/Blue. It's not universal hate, though, but the Vocal Minority on either side has been extremely loud on the subject.
The art style is considered pretty but many fans thought it looked ugly from the trailers. Similarly fans were upset by the fact it deviates from Pokémon FireRed and LeafGreen in many respects, especially the designs of Red and Blue.
The inclusion of game elements (Trainers using up to six Pokemon while Gym Leaders use a few; health bars) have fans split on whether they meshed well with a realistic Pokemon universe.
And when it was announced, people were butting heads over which was better: this, or the regular anime. Particularly when it came to their protagonists.
Bulbasaur, who was often suggested to be the best starter in RGB for beginners due to his strength against the first two gyms and resistant to the third, doesn't feature at all beyond a television shot of him at Oak's. While it'd be wrong to say the reaction qualifies as "broken", let's just say many who had Bulbasaur as their starter were... displeased.
Arguably, the premise of Red being a caring and loving trainer. While he certainly does show great concern for many other Pokemon, his own team members don't seem to receive as much attention. After being defeated by Blue's Squirtle, Red offers no consolation or caring to his Charmander, behavior that repeats after it evolves into Charizard and is defeated by Giovanni's Nidoqueen. While this may be a result of the anime needing to be condensed over four episodes, it is somewhat jarring to see that message contradicted blatantly, especially after all of the bonding Ash and Pikachu do in the main anime. This is elaborated on at The Cave Of Dragonflies along with other ways the special violates Show, Don't Tell.
Furthermore, Red's care for Pokemon seems a bit questionable considering a scene where he debates throwing bait to a Chansey or just throwing a rock at it. Sure, it was a game mechanic reference, but it seems odd that someone who talks about respecting Pokemon would consider throwing a rock at one. There's also the matter of one of Red's first Pokemon being a Spearow he captured. In Episode 4, he catches a Fearow to complete his Pokedex collection, implying that he only caught the first Spearow simply to complete the Pokedex and has never used it since. Of course he might have traded his Spearow for a Farfetch'd at some point.
Ensemble Darkhorse: After the Mewtwo from the 16th anime series movie sparked an Internet Backdraft, many fans enjoyed Mewtwo in this special, as it provided a third interpretation of the character after the two anime series Mewtwo - essentially, an uncontrollable and highly dangerous superpowered wild animal... just like any other Pokémon in the games.
Germans Love David Hasselhoff: Origins was hyped to oblivion in the West due to fans being fed up with the regular anime. In Japan, its TV ratings weren't spectacular, and it failed to outdraw a regular anime special starring Cilan and Brock. Naturally, Origins was available for purchase on iTunes in the West long before the regular anime.
Mewtwoshrieking like a maniac after Red throws his first Ultra Ball at it and it breaks free. It's like some nightmarish klaxon siren: not something a living being should sound like, and the Nightmare Face does not help at all.
It's Short, so It Sucks : While sucks might be too strong of a word, many fans were disappointed that the OVA was only four episodes, and that only a couple of the Gym Leaders got highlighted among other rushed moments.
It Was His Sled: Spoiler alert - Mega Charizard X exists! This came as a surprise when the special first aired, although his appearance in the special may still come as a surprise for some.
Jerkass Woobie: Blue. Sure, he's much more of an asshole than he is in the games, but you'd be lying if you didn't want to give the poor guy a hug at some point—especially during, and after, his last battle with Red.
And it doesn't stop there, either. After his ill-fated battle against Mewtwo, in which his Pokédex was crushed after his Blastoise fell on it, a bandaged and bedridden Blue can only watch as his rival hands in his completed Pokédex to the professor.
Misaimed Fandom: The special was meant to be a tribute to the video games, but some persons latched onto it as being the "true" anime, putting Red on a pedestal while bashing Ash.
The moment when Blue's Squirtle uses Bite on Red's Charmander. Squirtle chomps Charmander on the neck, and for about ten seconds, you hear it screaming. The flame on its tail start to die before Red retrieves it. The screaming was toned down in the dub, though it leads to a different kind of Nightmare Fuel.
They animated the "Do you believe in ghosts?" scene; when the woman asks the question, Red answers with "Not at all, I don't think they exist." nervously. The woman responds with "The white hand on your shoulder, I'm imagining that right?". Red laughs nervously and replies "Could you please stop joking around?", and when Red opens his eyes, she and her friend are nowhere to be seen. Worse still, if you look closely, Red actually does have a white hand on his shoulder◊.
Remember hearing about the Marowak killed by Team Rocket? Well here, you actually see it. Sure, it cuts away from the actual killing, but they do not skirt the implications at all. Oh, and even though they cut away? You can perfectly hear Marowak's lovely blood-curdling scream. The pitch is almost human, which just makes it more painful and haunting to hear. Like when Charmander got bitten by Squirtle, this was also downplayed in the dub.
When Giovanni's Rhyhorn OHKOs Red's Victreebel, you can see a puncture wound in Victreebel's stomach.
Seeing Blue in bandages after his encounter with Mewtwo.
Mewtwo's silhouette wreathed in flames is nightmarish.
Pandering to the Base: Many aspects in Origins seem to be directly based on popular fandom opinions and polls, including:
Charizard's role as the main Pokémon, and Pikachu having little more than a cameo. Charizard got first place in an IGN popularity poll in 2011 and is essentially the biggest Breakout Character in the franchise, with Series Mascot Pikachu placing 48th.
Mega Charizard X debuting as a Fire/Dragon type with Zekrom's color scheme. Zekrom was a major fan-favorite in Generation V, partly due to its colour scheme, and many fans were clamoring for a Dragon-type Charizard.
The Darker and Edgier nature of the special, with more intense violence. While the dub invokes Never Say "Die" for some odd reason, the implications of the mother Marowak's death are not skirted or censored at all.
The omission of Pokémon Speak, which many older fans criticize in the main anime series for being annoying and cartoonish.
Red actually catching all 150 Pokémon of Kanto Region, which is a common point of criticism on Ash for not living up to the English's slogan.
Team Rocket actually showing up and pulling off the heists they did in the original games, which did not exactly happen in the anime.
The confirmation that Mr. Fuji from Lavender Town is the same person as the Dr. Fuji that worked on the creation of Mewtwo. This was previously hinted at on a sign found on the event-only Faraway Island in Pokemon Emerald (though only the Japanese version had the name on the sign).
Subbing vs. Dubbing: Some people love the English dub (Bowdlerization aside), others outright hate it. Notably, Dogasu, usually a harsh critic of English Pokémon dubs, actually said that the dub is really good, to the point where he warned people to avoid fansubs of the special due to their generally low quality.
Tear Jerker: Cubone reuniting with the ghost of its dead mother, as well as the flashback telling Cubone's story. See the Nightmare Fuel entry above.
Woolseyism: Despite the Lost in Translation matter regarding Blue's shirt losing its reference to Pokémon Green Version (and Pokémon Leaf Green Version, by extension), the English name change of "Green" to "Blue" allows both Red and Blue's names to match the original English paired versions (Red and Blue) as well as the colors/elements of their starter Pokémon (Charizard and Blastoise, respectively), the latter of which being something that the Japanese version of Originsdoesn't do.
Although, in the second case, Green/Blue vocally denies any attempt to make his Pokémon choice match his name, unlike Red.