I wrote a recent blog post:
It is tempting to force a player to follow a strict, linear path. I know. It's something I've caught myself doing on the game I'm curently working on. Even with more or less freedom movement, I've found myself attempting to direct the player. This is not the way to do things in an open environment. How can one expect players to be intelligent if one treats them like an idiot? Developers have to trust the player. Otherwise, we are simply pandering to the lowest common denominator.
I think this goes for the matter being discussed here. It's time to trust the player. Tell the narrative you want. The player will either be carried along or they won't. It's not a player problem, it's a writing/presentation problem. If you're not confident in your narrative, how can you expect the player to be?
That is the problem with the mainstream game developers and even indie games. They treat the players like idiots. Of course, there will always be those who don't "get it". So what; you can't please everyone.
It's all stylization of one sort or another. We rarely think about the structure of prose, 1st person, 3rd person, etc. As readers, we are exposed to it from a very early age. But like any art, it's an artificial structure that evolved to help make it easier to follow writing. The (not)games form needs developed more when it comes to narrative and character. Prose isn't obvious. Neither is WASD or d-pad and buttons A, B. Or unusual amnesia. These are conventions to make things easier, not just on the author but the player/reader as well.
These "problems" are the same faced in any artform. Especially in scifi and fantasy. Because the settings and situations are unusual, you have two options as a writer: amnesia or extensive exposition early on. There is a third option but it is much more difficult but is much more elegant; ease the reader into the world as you tell the story.
I don't have any concrete answers but I don't think this matter is as problematic as you think. Don't be afraid to lean on cliched conventions if necessary. Trust yourself and the player.