The chest mechanic is not the only mechanic forgotten, but actually I'm not sure forgotten is the right word for it. More like some elements of the game are used to limited quantity for a chapter or a few before dropped for the rest of the adventure, maybe to help keep the pacing up, fend off repetition, etc.
Other examples of this include the invisible enemies (who only appear for a brief part of the game then never again show up), the poison fog rooms in Chapter 7, the lightable environment objects such as hay stacks and oil in chapters 2-4, and so on and so on.
Another thing I noticed is that the game has a lot of the same sort of traps for most of the game, but then suddenly introduces a few new traps in Chapters 13 and 14 that are only used briefly as they show up so late into the game.
All this isn't particularly a flaw per say as the game has so many ideas and works many in and keeps up a good variety of ideas to avoid the game from becoming old or samey during its 13-17 hour run, but if you really think about it, it does seem like some mechanics could of been used more or used in some more creative situations rather than just appearing briefly and then being gone. It almost reminded me of Super Mario Galaxy 2 in that way, so many ideas in different areas of the game but very few of them are actually expanded on, which isn't really a con as it makes up for it in variety and solid core mechanics, but it might have been nice to see some of those ideas more developed.
