Patashnik, that's a pretty well thought-out analysis. Just a couple random thoughts you've inspired:
I know there's been complaints about Juste's sprite and color scheme, but they've honestly never bothered me. Perhaps it's because I've never gotten into sprite-making, but more likely it's because I'm colorblind. I probably don't see his sprite as vibrantly as most people, so to me it was never a problem. My colorblindness also gives me problems in the map screen of this game. I have trouble seeing which rooms are which color until I look really closely.
As far as the dead ends, I actually like that aspect of this game. That's the part I like about the Metroidvanias; you can see just beyond where your way is blocked, and you know you can get over there eventually, but you have to explore more to do it. So much more interesting than a locked door, but the function is the same. Although it does make the game more confusing, especially once you have two separate castles to explore. I can see how it's a kick in the pants to explore a big, new area, only to dead end at one spot with no new items of significance to make the trip worthwhile. Probably the biggest offender is the first time you can explore the topmost portion of the chapel. You trek all the way up there, pretty far from a save point, only to dead end at the locked door leading to the castle keep, erm, top floor.
I never thought about the teleporter thing, how there are two different types of teleports and how that really doesn't make any sense outside of gameplay confines. But I never did like how the first time you go through a teleport, Juste says something to the effect of, "Something feels different about this place." The game designers meant that to be a hint or a foreshadowing of the dual castle thing, but I just thought it was a big "duh" moment. Anybody who knows anything about teleports should understand that going through one puts you in a different place. I thought Juste was just stating the obvious, that he had just teleported to a different place within the castle, but I would have thought a little differently about the comment had the developers worded it more appropriately.
As far as the music goes, the general banner of the HoD soundtrack supporters is that the problem isn't with the compositions, it's with the sound quality. And that's true to a point, but there are some tunes that, in my point, are just bad all around. The Luminous Caverns theme is one of these. The Wailing Way BGM is another, and the merchant theme is just trash. But the good tunes are still good enough to redeem the soundtrack, at least to the point where it's not deserving of the criticism that is usually directed at it.