So, regarding the plot barriers ... With the exception of the white ones, that do sort of arbitrarily disappear at a midpoint cutscene (I tried to place some near that point so it was easy for the player to see when it happened), I thought they were relatively clear. They're all color coded according to the bosses you fight, who each clearly have a primary color that they speak in, and most of their attacks use. They change color to match who you fight depending on your character, too. I felt that this was a concept fairly well-established in old games like Metroid. The first set is also only accessible after the player has most likely beaten the boss in the lower left, too. Even if they got the flippers and headed straight back to Lethe, I'd expect at that point they would have at least encountered the boss in the lower left of the labyrinth, if not beaten it. I'd think most people could piece it together. "I beat a blue boss, and now the blue blocks I see here are lowered, but there's still red ones remaining, and I haven't explored everywhere yet, so ..." I'm actually a bit puzzled by your objection here. I don't think it's as opaque as you make it out to be. I've designed with them in mind to demonstrate the concept just in case, and lots of old games have used this to a point where I'd expect most players to be pretty comfortable with the idea. With the white blocks, on the other hand, I really have no excuse and just sort of designed myself into a corner.
How far have you made it in the quest? When you talk about "metal diamond-shaped blocks," you're talking about the ones in the sky? They serve a pretty specific gameplay function that's demonstrated pretty quickly in an early-game area. I don't think a little mystery about their function is such a bad thing. I don't have a problem with a player seeing a certain gameplay element, going, "I wonder what THIS does ... Guess I can't do anything now," only to discover their function a bit later. Lots of games do this; not every game communicates exactly what something does the first time you encounter it, and personally I'd find it dull if everything were spelled out. Players are expected to find solutions to different kinds of barriers as games progress.
The theme I'm seeing here is that we may just have different philosophies on game design here. You seem to want everything's purpose and function to be very clearly telegraphed, while I think it's perfectly okay for the player to encounter a few "unexplained" things and then have those things made clear with further exploration and experimentation. Nothing wrong with that, I suppose.
As for the vanishing blocks ... I'm glad you liked that element. There's also some ways later in the game to help out players who dislike it, or for ones where the clues are a bit more obscure than they should be. Basically, Yuurei's answer to the super bombs in the Metroid series. I did try to provide good visual clues for nearly all of them (though I can think of a couple offenders), but I hope that I've managed a good balance for people who like hunting for stuff, and people who don't so much but are dependent on the powerups.
In any case, thanks a lot for playing. I do really appreciate hearing your thoughts on it.