Fez
Fez's later puzzles are genuinely puzzling, and some of the hidden levels are impressively, amazingly clever. But there are a couple of secrets that are just too clever, including at least one that isn't actually "solvable" in the conventional sense. Yes: I had to consult the interweb for a few solutions, and I'm OK with that.
This, in my mind, is what keeps Fez from being as perfect as Braid was. Having hidden secrets is great - and Fez's progression of mystery and reward is excellent, on the whole - but occasionally the intricacy and obtuseness is pushed just a little too far.
Progress: 100%