Castlevania: Dracula X
While Japan recieved Castlevania Dracula X: Rondo of Blood, fans in the United States had to wait two years to see Richter Belmont's adventure -- although the form we got it in was, arguably, quite flawed. Although structurally similar to its Japanese bretheren, featuring Richter Belmont once again on his way to Castle Dracula, Castlevania: Dracula X (referenced most often as Dracula XX) is a drastic reimaging of the original game.
The biggest change, and the one most people point to as its greatest flaw, is the fact that Maria Renard is not a playable character in this game. Although both games feature characters for Richter to find (four in the original, two in Dracula XX), Maria only serves to give the players the best ending in Dracula XX. Otherwise, unlocking her or not has little bearing on the game (and with Maria being one of the best features of the original game, excising her from the SNES version is a grevious issue). Considering the relative brevity of the game (nine stages total, but you probably won't play all nine of them in one playthrough), one has to wonder what constraints lead to Maria's removal.
Interestingly to note, though, is that the game did have one lasting difference for Maria: in Dracula XX it was established that Maria Renard was Annette's sister (Annette being Richter's betrothed). Maria being related to Annette was implied in dialogue in the sequel to Rondo of Blood, Castlevania: Symphony of the Night, with Maria being Richter's sister-in-law.
While the plot and basics of the game are the same, Dracula XX diverges greatly from Rondo of Blood in levels and level-design. Some levels are close stylistically (such as the two very different "Village Ruins"), but the order of many has been changed, and some stages are swapped out completely (Dracula XX sports the "Sunken City" instead of the "Haunted Ship" or "Docks"). All the levels are completely different in layout, including Dracula's "Castle Keep", which now doesn't even have the traditional staircase up, and features an end-room of tiny columns instead of the standards throne room (making that boss fight drastically harder).
And that points to another fan-commented "flaw": the game is substantially harder than it's PC Engine predecessor. Monsters are positioned in hard to reach places, but still can easily get you, and everything in the game is structured to make the game unbearably difficult to play. While most Castlevania games are hard, Dracula XX wasn't just challenging, but unfair. Actually bothering to make it through the game is considered an accomplishment by some.
All the flaws combine to make a game that was, fairly, removed from continuity -- even the designers considered the game to be a side-story/alternate-continuity retelling of Rondo of Blood. Even in the official compendium of all things "Dracula X", Castlevania: The Dracula X: Chronicles, Dracula XX was tellingly not included.