As I mentioned in my recent update, I'm working now on the puzzles in my Amnesia mod, and it's a curious feeling. One of the most difficult things in a game is integrating the gameplay and the story: I've seen many a game with an atmosphere and story marred by gameplay completely unsuited for it, or a game with great gameplay and a completely unrelated, pointless story. Unfortunately, I'd be being overconfident if I said I knew I was going to avoid these traps.
Complicating this is the fact that I'm working with Frictional's props and items, which provides me with a great toolset but also circumscribes what I can do with gameplay. One of the things that plagued the original Amnesia was a sort of hypertrophied version of Chekhov's Gun: If you saw anything that could be picked up, you grabbed it and could be reasonably confident that it would be used within a couple of levels. If you saw a lever, you pulled it. If you saw a valve, you turned it.
An aside: The puzzles weren't the sadistic fiendishness I've come to expect from adventure games--the only things I found truly difficult were a couple of slightly arbitrary bits where I got it into my head that one thing would work, it didn't, and I just kept trying it.
In many ways, this helps the game avoid the insane dream-logic that Old Man Murray skewered so many years ago. You don't have to set yourself on fire or use cat hair to construct a mustache, even if you do have to do some things that range from merely distasteful to downright grotesque (there's a reason that bone saw is in your inventory.) But there's also less of a sense of discovery each time you solve a puzzle--it feels a bit like marking time, unlike the Penumbra series, which really made you work for your progress.
Overall, however, I'm all right with the Amnesia puzzles, primarily because they really do fit the atmosphere of the game so well. The beauty of Amnesia wasn't that the puzzles were hard, it was that the game scared you so much that even simple things became difficult, because you were running around hiding in the dark from monsters that weren't even there. It's not Dear Esther by a long shot, but Amnesia verges in places away from traditional gameplay and towards an interactive story based on atmosphere.
Part of that atmosphere, however, was that of a place that was barely lived in. There was nothing in Amnesia to suggest that anyone but you, Agrippa, and the Baron regularly inhabited the castle--the few flashbacks were of prisoners, and even those were of people who had been brought to the castle, not those who lived there. I'm trying to provide a different feel--one of the castle as a recently-living place, a place with people whose worlds were, even through the siege, vibrant and full. And that may require a different kind of gameplay.
