Metal Gear creator Hideo Kojima has went on to state that he felt the original two MSX 2 games in the series, Metal Gear (1987) and Metal Gear 2: Solid Snake, did not age very well since the original Metal Gear Solid is essentially (gameplay wise) a remake of them and even went on to state that he regretted that he made Metal Gear Solid a sequel to those games instead of a reboot.
The original Hitman: Codename 47 seems to have — many would say quite deservedly — become this. It's the only game in the series not to have been released on a console — a more typical platform for stealth games — and is not included in the Hitman Trilogy collection (Except for the Steam version, mentioned below), whose very name implies that there are only three games in the series. IO and Eidos haven't yet publicly disowned it, but that may well be because they'd have to acknowledge its existence in order to disown it...
This is half the point of the entire game that is Hitman: Contracts (which is a part of the trilogy): in a lot of ways it's a remake of the best parts of Codename 47.
Oddly enough. The Steam release version of the Trilogy switches out Contracts for Codename 47 because of song licensing issues.
Persona was one of Atlus' first attempts to localize an RPG in the North American market, but the end result was hopelessly screwed up. As Atlus USA has gotten much better over the years, the company eventually made an announcement that they were going to attempt a proper localization of the game for its PSPUpdated Rerelease, more than a decade later.
Hudson Soft, creators of the Bomberman franchise, have all but disowned Bomberman: Act Zero, making fun of it in a promotional video for Bomberman Live.
Contrast thesearticles they made, in which they attempt to defend the game in reaction to the fans' complaints.
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 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, Square Soft themselves published at least a couple PC hentai games in the early 80's, which they have never mentioned again.
Square also seems to not acknowledge the existance of Rad Racer, which was actually a good game.
In the 8-bit era, Code Masters was a major producer of unlicensed NES games (some of which were ports of their C64 games), although a few of these, such as Micro Machines, were actually fairly good.
Nintendo would like you to believe that Hotel Mario and The Legend of Zelda CDi games don't exist. It's possibly the reason Mario and Link barely (if ever) talk and possibly why Nintendo stuck to cartridges for another generation...
They would also like to pretend that the Virtual Boy doesn't exist either. Most people who have actually played one agree with them.
The Reality On The Norm game Disappearance Time. The author was so embarrassed that he went back and updated the game by adding snarky commentary throughout.
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 enthusiatic to talk about Akira. Worse still, attempts to contact that heads of development company ICE Software are met with profanity-laden resistance.
Seamus Blackley is best known as the creator of the X-Box, 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.
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 level.
In fact, part of the reason that Ocarina of Time got an Updated Rerelease on the 3DS was so Aonuma could fix the problems with the Water Temple.
If you look at Blizzard Entertainment's website, about half the games they ever developed are not listed.
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 Traveller's 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 is not a sequel to Daikatana.
