Every criticism of this game I've seen on these boards have been very constructive. This is the kind of thing a good artist loves to hear, and is all part of the ongoing dialog between those who create and the people who pay for and consume their work.
I think we're having all these threads about the mapping system because it does a few odd things that if either one were more transparent, the other would be largely irrelevant. The first one is the lack of "fog of war" progress tracked on all areas. We all know that this is a technical problem in the game as of this writing, but if implemented you could glance at the map and know where you had been. If, say you'd obtained an ability and we're looking for places that you were previously blocked from, this would narrow down where those barriers might be immensely.
Second, the game already has a discovery based icon system but it's used in a way that doesn't make much sense. It tells you where a boss was after you've beaten it, and found memories but I don't see why you'd really need to know that other than not to wander down that way again. Perhaps these are meant as check marks of a sort. It also marks some ability based barriers like the nature form "blue dome" shortcuts but not others, like blue crystals, darkness, and impassable currents.
If either of these things we're as suggested, these threads probably wouldn't exist and the map system would not be mentioned as a strike against the game in any of the reviews. As it is, it's in almost all of them.
Paper is good for things like inkblot listed, but when you want to notate something like where a blue crystal is located, things get a lot more involved. You either end up drawing a map, which would be difficult and time consuming in a game like this or you give yourself directions that probably make a lot of sense when you write them, but may not make so much when you try to follow them 10 hours of gameplay later.
Some form of manual map notation system would in no way take away from the experience, and would be more in line with modern game design conveniences. Marking the map up yourself is fun and very satisfying when it pays off. For some it would be even more fun than wandering around later on trying to find the x or y that you recall seeing. But if you prefer that, you wouldn't have to use it. It's an excellent compromise.