I've always disliked gameplay which removes atmosphere and this is particularly rife at the moment. Gameplay often feels gimmicky - has a twist, a 'unique' component to make it stand out from the crowd. But gimmicks don't sell games - fun gameplay does. It's not that unique gameplay approaches aren't important, it's that too many games make this the dominant feature - rather than a feature that contributes to the overall package. This can be quite rife in indie games because it's often conveyed in such a way that it breaks the 4th wall 100% of the time. Braid is an example of an indie game which had a unique feature (2d platforming time reversal) that was both inherent in the game design but not the sum of the game as a whole. People who've played Braid deeply don't tend to say 'oh Braid, that time-reversal game', they say 'oh, that game Braid which was multifaceted and which Also had that time reversal mechanism which did my head in'. Rather than being a gameplay element which happens to involve a character, it's a game about a character in a unique environment (and as long as the gameplay element is inherent to that environment and fits, it doesn't disturb the 'inner world' of the game).
The best way to build unique or new ideas into a game without disturbing a sense of atmosphere is to step the player gradually into unfamiliar gameplay elements, rather than spelling them out straight away. If you do spell them out, it can be a better idea to do it away from the game proper. The 90's practice of giving the player a game manual rather than 'hit X button now' in-game was actually quite valid in terms of teaching the player without disrupting the sense of atmosphere - as it created a cognitive gap between the gamer learning and the process of them them actually playing the game. Tutorial levels can be another way to illustrate the gameplay process without breaking the 4th wall in-game.
Games with unique gameplay mechanics which get it right:
Braid (indie, payware) - For the reasons mentioned above.
World of Goo (indie, payware) - Although the gameplay mechanic was unique, so was the atmosphere and stylistic delivery of the world - you didn't feel like you were completing abstract puzzles in a non-conventional game, you felt like you were working towards some sense of completion in an arbitrarily crazy, slightly unsettling little world (of goo).
Games with unique gameplay mechanics which get it wrong:
Bulletstorm (AAA, payware) - Yup. Nothing to see here. The game made such a big deal out of it's central feature - the grab-you/pull-you arm-claw-lightning-thing - that it forgot to emphasize that it was actually a complete game outside of that feature. As a result it comes across as gimmicky and incomplete, alternating between different set-pieces without ever achieving a central 'feel'. Also, it's tendency to inadvertently contrast despair and bloodshed against light-hearted arcade-ey gameplay and slot-machine sound effects was incongruous, to say the least. Don't get me started on the dialogue.