Nobody can make a perfect game. Some people, such as Shigeru Miyamoto, regularly get close, but no, not quite, that boss turns out to be more of a boring grind than a fun challenge, and you have to ride way too far between those two places. So this thread is for awesome games, but with parts that sucked ass.
Sonic the Hedgehog was about as much fun as a game got in 1991, except for the second world. The Marble Zone was annoying as all Hell, since having spikes everywhere tends to discourage use of Sonic's main attribute: speed. Similarly, the Hill Top Zone in Sonic 2 can be counted as annoying with its lava, but the real trash in Sonic 2 is the fucking shitty Special Stages, especially how you return to the main game and all your Rings are gone. Over on the Nintendo side, the Frog Suit in Super Mario Bros. 3 is extremely limited in use and a real drag in most levels. The original Legend of Zelda had no way of knowing whether you were going in the right direction, so all too often you'd wander into a high-level dungeon before you were ready, and it was just too hard to get the required Rupees by killing monsters. Third parties weren't exactly innocent either: the Laser from Contra was so fucking stupid, you mean I lost my Flamethrower for this shit?! And can someone tell me why Goro from Mortal Kombat was stronger than his teacher, who happened to be the final boss of the game? Shang Tsung was useless in #1.
Fast forward to modern games. Zelda has long since fixed its early problem with being too open-ended, but in Twilight Princess it's just too far from one point to another (but hey, at least it's not as bad as in The Wind Waker, which was just as great a game but had it even worse). Assassin's Creed, while it tells an awesome story, is just a bit too repetitive to have any replay value. And, um, I honestly haven't played many really good modern games so I wouldn't know much more.
So, anyone else have a game that would be perfect if not for that ONE FUCKING PART that nearly ruins the experience?