Eye Of The Beholder 3: The Mausoleum. It's a 2-level dungeon at the start of the game that not only features some of the most fiendish puzzles, but also some of the toughest enemies, including the only monster in the entire game that drains levels from your party. The problem? There's no need to enter the Mausoleum at all, as no progress-vital items are kept in there. What's worse, the ultimate reward for clearing out the Mausoleum is the Rod Of Restoration, which you'll only ever need...if you went through the Mausoleum! :X
The first Ravenloft game has a similar problem as EOB3, only you have to go through almost the entire game to get your hands on the Restoration spell, and kill large groups of level-draining monsters first. But once you can cast the Restoration spell, you barely need it again.
Ultima 9: Finding out that Britannia has...
shrunk since you were there last.
(Actually, U9 has loads of bad moments, but that one stuck out the most for me.)
Ultima 8: Discovering that a pretty atmospheric piece of fluff in the manual was actually just a thin cover-up to conceal that Ultima 8 was technologically
inferior in many ways to Ultima 7.
(Again, U8 has loads of bad moments. Finding out that the cloth map is useless is another good example.)
Ultima 7, Part 2: There's a bit in Moonshade where the only way to progress further in the game is to gossip with a specific shopkeeper about a specific person, but only
after this specific person has appeared in Moonshade. This gives you a piece of info that you must use to continue in this all-too linear game. I got stuck on this for months back when I originally played Serpent Isle, because there isn't even a hint or a suggestion on what must be done to continue.
Arcanum: Discovering that the latter part of the game is not even half as interesting as the first part. "Rushed" doesn't begin to describe it.
Albion: Learning that you pretty much have to mindlessly grind levels at key locations just to complete the dungeons needed for the main quest.
Anachronox: The "magic" system. It has so much potential and possibilities...and yet you're good for the entire game with the simple DPS and heal spells.
Anvil of Dawn: You can't rest. Makes the whole game tedious and sluggish.
Baldur's Gate 2: Pretty much the entire Throne of Bhaal expansion except for Watcher's Keep.
