I just started playing, and my thoughts basically mirror yours. So far, the game feels like a hardcore indie version of Ico, mirroring all of the problems it had 15 years. There's so much to like and adore about the game, but unfortunately most of them aren't connected to the gameplay. The atmosphere, art direction, and music are all top notch, but whereas Ico was easy enough to get through the bad encounter design, Hyperlight is challenging enough that its bad parts can stonewall progress, compounded by the horrific checkpointing. I started in the East, and there was one especially bad stretch where I was stuck clearing the equivalent of 4–5 rooms, but because I died in an arena that wasn't its own discrete one, I had to redo everything. The basic mechanics feel really good, even when restricted to slashing and dashing, but like you said, some arenas are just slathered with enemies. It's one thing when you're playing a bullet hell composed of meticulously-designed patterns; it's another when everything's random, which can lead to unavoidable attacks. It's yet another when the basic tools aren't suited for crowd control.
It doesn't help that the game's iconography and non-written communication are good enough to justify having such scarce tool tips. The bomb preview shows you throwing something and it having an area-of-effect, but there weren't any enemies or obstacles present. So it has an area-of-effect, but does it damage? Does it stun? Is it an EMP for disabling weapons? I dunno, better spend eight skill points to find out. That also extends to the map, like you said, but also to things as fundamental as healing. Nowhere have I seen the game show that using a teleporter resets everything. Even throwing a med-kit right before reaching the first teleporter and having it visibly refill after activating things would've helped.
It's also ridiculously easy to take damage or die, which just makes me more and more confused about the checkpointing and healing. From the east side, the punchers and ninjas don't flinch from attacks, which means especially for the punchers that have three HP, it's very easy for them to get off a punch before dying, especially when in swarms. There's also cases where dashing across platforms doesn't properly magnetize you, meaning you can plummet into the water by an error of a few pixels from the analog movement.
Being arcane can evoke feelings of mystery, of discovery and wonder, but it can also mean being really, really obtuse. I'm six minutes away from not being able to get a refund, and I'm really debating if I should drop the game and pick it up again once it's cheaper.
The East is littered with frogs jumping out of the water with no sign that they were ever there, and there's one encounter full of frogs that's just a clump of them jumping around. It'd be nice if I had other tools to deal with them, but I don't. I appreciate not being blockaded from certain paths if I want to pursue them, but the developers need to communicate that I'd be better off going in a different direction. Nothing about the encounters being difficult feels deliberate the way stumbling into an area with enemies ten levels higher than you does. It feels like I'm expected to compensate for their shortcomings with bone-headed perseverance.