Persona was one of Atlus' first attempts to localize an RPG in the North American market, but the end result was as mess. The company eventually made a proper localization of the game for its PSPUpdated Re-release, more than a decade later.
In the early '80s, before they started publishing for consoles, Enix released some games for PCs. Several games they published were hardcore hentai games where, if you lost, you saw the girls' mutilated and tortured bodies. As you can guess, Enix (now part of Square Enix) is a bit dodgy about these games now, and this part of their history doesn't pop up much in bios of the company. On a related topic, SquareSoft themselves published at least a couple PC hentai games in the early 80's, which they have never mentioned again.
Nintendo tried to pretend the Virtual Boy didn't exist for a while. However, it's featured in Super Smash Bros. Brawl as part of the "Chronicle," a near-complete list of games published by Nintendo. Interestingly, the Virtual Boy has started to become something of a Running Gag with Nintendo, being an obtainable item in Animal Crossing: New Leaf which pokes fun at its red graphics, and a collectible treasure item in Tomodachi Life that only exists to be sold.
The video game adaptation of AKIRA is wrought with this: as well as being one of the worst games released on the Amiga, the details of its development are a little nightmarish. Some of the devs have since gone on to bigger and better things: Martin Blackmore works with the Kinect for Microsoft now, and Anders Johansson is a developer for the Need for Speed series, just to name a couple. Neither of them are all that enthusiastic about Akira. Worse still, all attempts to contact the heads of development company ICE Software were met with profanity-laden resistance.
Despite record sales and characteristically positive reviews, Ken Sugimori, the artist for the series, felt Pokémon X and Y were too complicated and strayed from his original visions, vowing around the time of the games' release that Generation 7 would be simpler.
Seamus Blackley is best known as the creator of the Xbox, but before that he conceptualised and worked on Jurassic Park: Trespasser. Blackley is so ashamed of the game, he refuses to bring it up or talk about it when asked.
Capcom has said that Street Fighter has not aged well, mainly due to how the game's special moves were very difficult to execute.
Though Shigeru Miyamoto and Eiji Aonuma were pleased with The Legend of Zelda: Ocarina of Time as a whole, they've gone on a limb to apologize for the Water Temple. It's especially telling that Aonuma wasn't the series director yet but still felt the need to apologize for that dungeon... because he was the game's primary dungeon designer.
In fact, part of the reason that Ocarina of Time got an Updated Re-release on the 3DS was so Aonuma could fix the problems with the Water Temple.
Aonuma has also said he feels the game isn't that good in retrospect, due to the technological limitations of the time.
Corey Burton feels this way in regard to how he voiced Shockwave in at least one Transformers: War for Cybertron commercial, he didn't think of it too much at first, but regretted doing the commercial because it made Shockwave feel incredibly Out of Character ("When your hit percentage exceeds mine, you may choose the soundtrack!"?).
Some of the developers at Travellers Tales absolutely hated working on Super Monkey Ball Adventure. At one gaming forum that one of the developers posted at, a member posted how he was thinking of trying the game out again and the developer replied "never ever go back to that game again".
When mentioning that he was working on a new game, John Romero went so far as to announce that it wasn't a sequel to Daikatana.
Believe it or not, Keiji Inafune feels this way towards the generally well-liked Super Adventure Rockman. He doesn't feel it's of low quality or anything like that, he simply feels its plot and tone were made way too dark for a Mega Man game. He also doesn't like Mega Man 3 very much due to its strained development and him feeling its gameplay was overly complicated.
In an interview with SiliconEra, Haru Akenaga, then-president of NIS America, stated that he was dissatisfied with the PlayStation 3 game Last Rebellion. He only released it due to a previous relationship with developer Hitmakernote NIS published Blade Dancer: Lineage of Light in the U.S., and tried his best to convince his team not to promote it beyond the typical "new release" press statement.
Grasshopper Manufacture worked on Shining Soul and the sequel; however all references to this have been removed from the game's credits. Only reluctantly will Suda51 admit that the studio worked on the sequel.
Capcom would really, really, really like everyone to forget Devil May Cry 2. Aside from making sure none of the subsequent games touched on 2's story in any way, shape or form (3 and 4 were both set before 2, and Dm C Devil May Cry is a complete Continuity Reboot), they actually include a few Take Thats in Viewtiful Joe. For instance, Dante flat out says he doesn't know what Alastor is talking about when Alastor mentions the events of DMC 2, while Trish coyly suggests that the "Dante" seen in the game was actually his friend Enzo in disguise.