Ganondorf Syndrome is when a character who is popular with their home fanbase is less popular in Smash. This can be for several reasons, including being a clone or having an ineffective moveset. Coincidentally, all three "full" clones in Smash 4 (Dr. Mario, Lucina and Dark Pit) and all three Kid Icarus characters suffer from this. See the category for Ganondorf Syndrome sufferers.
At the opposite end of the spectrum is Jigglypuff Syndrome, where the character is more popular in Smash than in their home fanbase.
A recurring opinion for these types of characters is that Custom Moves improve both their competitive viability and their enjoyability in general. Examples include Ganondorf's Warlock Blade, Charizard's Dragon Rush, and Palutena's everything. The "true" clones get no such benefit.
One of the most iconic and badass video game villains of all time and the phenomenon's namesake, Ganondorf is often derided in Smash for being a clone of Captain Falcon. Many cite him as one of the most nonsensical clones of all, due to his frequent use of magic and swordplay in his home series rather than bare-knuckle Falcon-style brawling. He remains a clone all the way up to SSB4, but at least he picked up a couple of unique moves (and even a sword attack) along the way.
Despite this, Ganondorf (especially in Smash 4) has a cult following for being the "King of Disrespect", as a low-tier character who can nonetheless "disrespect" foes with his extremely flashy and hard-hitting attacks. A common debate is whether "de-cloning" Ganondorf would be a good thing or not, since a few people are used to his cloned moveset and enjoy using it; his customs, while still variants of his shared specials with Falcon, are different from Falcon's, with Warlock Blade being the best example.
Overall, Smash Ganondorf and Zelda Ganondorf are very different beasts. Zelda Ganondorf is widely renowned as one of the greatest villains in gaming, while Smash Ganondorf shatters the base between those who love him for his dank memes and fun and disrespectful moveset, and those who hate him for being the single most unfaithful character in the series (with a large amount of uncreativity to boot).
Charizard is a rather infamous example of this phenomenon. In the Pokémon fanbase, it's extremely vocally loved (especially by genwunners) and constantly wins popularity polls. While it did have some base-breaking of its own due to hype backlash, constantly overshadowing any Pokémon not named Pikachu (even its fellow Kanto starters), and serving as the poster child for said genwunners (who are a highly reviled portion of the fandom), there's no denying that it's one of the biggest and most popular icons of '90s gaming culture.
Meanwhile, in the Smash fandom, Charizard had a rather unspectacular debut as a member of Pokémon Trainer's team in Brawl - mind you, this was before its fanbase emerged in full force. Not only was it a clunky third-of-a-character that couldn't be played on its own, it was also a generally lousy and awkward character in its own right.
Come the prerelease period of Smash 4, and Game Freak was recognizing the Zard's popularity, giving it things like two Mega Evolutions and featuring it in a ton of animated specials. So naturally, as evidenced by its big entrance complete with tagline, its solo debut would make it one of the most hyped Smash veterans, right? Wrong. Unlike Mewtwo, who had a similarly lackluster debut in Melee, Charizard didn't have the "luxury" of being cut from a game and becoming a sacred cow among fans who missed it. All that people remembered was the clunky lethargic lizard from Brawl, and flocked to the flashy new ninja frog instead. The game's release didn't help matters much, as Charizard was still considered a rather lame character to play and spent a rather long time as a bottom-tier character; in fact, in the early days of the metagame, it was considered the worst character of all and was rather unpopular for it, with people arguing that Charizard was ultimately an unimportant character that people shouldn't hesitate to cut.
However, come Mewtwo's return and lots of balance patches, and the Zard's reputation was saved in a lot of people's eyes (it even made it out of the bottom tier in the third tier list!). While Charizard is still nowhere near as popular with the Smash fandom as it is with the Pokémon fandom, it evolved into a generally accepted and respected character overall, and Smash fans recognize its importance to the point that there are legitimate arguments over whether it or the much more popular, viable and reputable Mewtwo deserves its Smash status more.
Yes, Mr. Video Game Himself suffered from this, at least before the SSB4 metagame developed. While Mario is the most iconic video game character of all (and the most popular with general/casual audiences), many believe his moveset in the Smash series to be very boring and basic (especially in Brawl where he was one of the worst characters), with his only unique/gimmicky move (FLUDD) coming from an ancient GameCube game that nobody really liked. Smash Mario is so widely viewed as being "the character you ignore" that it isn't funny, unfortunately for the poor plumber. His becoming a legitimate top-tier character in Smash 4 (while keeping the same moveset) did help a bit.
In his home game, he's just Mario in scrubs. In Smash, he's just Mario in scrubs... taking up an extra character slot. Go figure.
Very popular with the Fire Emblem Awakening fanbase and frequently wins popularity polls as well; however, she is a less effective clone of Marth in Smash. Although her being a clone makes sense due to her impersonating Marth in her home game (and the real Marth in Awakening being a headswap of her), she is still rather divisive among Smash fans, with some people defending her due to her role in Awakening, her attractiveness and her cute dorky personality in Awakening, and others calling her the second-worst newcomer next to Dark Pit (third-worst if you count Mii Fighters). Even worse is that her Custom Moves... are also copies of Marth's.
Note that this has nothing to do with Awakening or its characters being unpopular, as Lucina's friend/ally/potential husband or mother Robinspent some time as popular newcomer on the board (maybe the most popular character on SmashFAQs in general), thanks to his/her very unique moveset that's pretty much the opposite of Lucina's. In fact, Luci is most well-liked of the three "true" clones in Smash 4 - unlike most of the other examples on this page, she's still generally a popular character in Smash, because waifu.
Over time, Lucina experienced two extremes of sorts. In summer 2015, she was a bottom-tier character and widely hated as a scapegoat for "too many FE characters", which was only worsened by the introduction of the King K. Rool Mii costume and the subsequent fandom rivalry between Fire Emblem and Donkey Kong, and it was universally believed that Robin and Ike were objectively more important to the FE franchise than her. On the other hand, when Corrin (a unique and viable DLC character) was announced, they took Lucina's place as the FE punching bag, as people began to recognize that the development time and creativity that went into Corrin was far more of a "waste of potential" than the very little effort it took to add Lucina, especially since people were expecting more ballot characters. Add to the fact that Lucina became a high-tier character in March 2017, and her hatedom now pales in comparison to some of the other things out there.
Believe it or not, the most hated Smash character of all time was fairly well-liked with his home fanbase, mostly due to his being able to show more of a personality and his relationship with Pit being fleshed out. In Smash, he's both a clone and a palette swap, and a stereotypically "edgy" young teenage character similar to Shadow the Hedgehog and a zillion shitty OCs out there.
Despite being SmashFAQs' most wanted choice for a newcomer for a time (beating even Ridley), the Goddess of Light isn't nearly as popular as she once was (and still is with Kid Icarus' own fanbase), in part because she is accused of being a prime example of Sakurai bias for three reasons:
- Her gimmick is having 12 unique Custom Moves, while other characters (other than the widely-hated Mii Fighters) don't get the same - even Ganondorf's Warlock Blade is just a Warlock Punch variant;
- Kid Icarus getting a newcomer in the first place while Metroid, Donkey Kong and The Legend of Zelda didn't get any (despite Palutena being an extremely popular choice);
- Being announced at E3 along with the more "special" Pac-Man and Mii Fighters.
Additionally, Palutena's default moveset is generally regarded as boring and ineffective (she even has yet another counter!). Her customs fare much better, seeing as it's her entire gimmick, but they can't be used online "With Anyone" and a few fans label them as lazy copies of other characters' moves (despite their actually originating straight from Uprising). Oh, and people find her parts in Palutena's Guidance to be among the most boring (most of what she says amounts to telling Pit to use the Guardian Orbitars... not that people found the Guidance itself much better). Nowadays, her fanbase is mostly stereotyped by Perverted Palutena Fanboys (including Sakurai) rather than Smash fans in general.
Wario Land Wario was a pretty gross guy, but his main defining traits were his strength, his invulnerability, his pig-headedness and his willingness to do anything (good or bad) to satisfy his greed. WarioWare Wario was pretty much the same (and was even shown to be able to run his own company and scam people), but his humorous aspects were played up a bit. Then Sakurai decided that Wario would be the perfect potty-humor character to put in Smash and that his moveset should be so original that it shouldn't take anything from Wario Land at all... Did we mention he's gross?
As an aside, Sakurai almost included Wario in Melee as the Mario clone rather than Dr. Mario. Whether this would have been better or not is up to the reader.
Pit himself, despite being a highly requested retro newcomer for both Melee and Brawl (pre-announcement, of course), has now undergone this as of this game for a few reasons.
- He's the main character of the Kid Icarus series, so people group him with its apparent overrepesentation.
- He's promoted over Fox, Marth, and Olimar (among others), all of whom are the main characters of series bigger than Kid Icarus.
Despite this, Pit is generally popular in his home series, and, once more, he was for quite a while in the Smash fanbase (enough to get a revival, which in turn caused this mess, ironically).
You'll notice that many of the characters here suffer from Ganondorf Syndrome because they have ineffective and poor playstyles, with Charizard and Lucina probably being the best examples.
Diddy Kong, however, is the exact opposite of those two: instead of a cool character who happens to be underpowered, he's an uncool character who happens to be overpowered. Other than Donkey Kong Country fans, nobody in their right mind enjoys playing as or against an annoying squealing monkey who throws bananas everywhere and mindlessly hoo-hahs his way to victory in every match.
Speaking of DKC fans, that's where the Ganondorf Syndrome sets in. Diddy was actually one of the most requested and sensible newcomers for Brawl, as the second most popular Donkey Kong character behind DK himself. He is far more hated among Smash players at large than DKC fans, many of which legitimately enjoy playing as him.