This is where I disagree. I get
she is on a mission and knows what she's doing, the problem is
I don't know what she's doing or even who she is.
I am not in any way asking for NPCs to chat with or frequent radio dialogues with my guy-in-a-chair. I literally just want to know
what the dragon is and why she followed it to the planet. We got the short text blurb about the distress signal so we know why we went to the spaceship, but nothing after that. That's literally all I want: even just a text blurb that says "the dragon is X and I need to follow it because Y." It's a fundamental aspect of storytelling that you need to present a motive in order for the audience to care about anything. I have no motive to follow the dragon or go to the planet, so I cannot care, which makes it very hard to feel engaged in exploring the planet.
So all you wanted for the story was a "Captain's log" type intro (to steal a Star Trek reference)? I suppose that's fair. As a caveat though, keep in mind that this is originally a Gamecube game, and instruction manuals still existed back then. I just dug mine up and checked... there IS a backstory listed there which would have given you what you need. Yes, Remastered doesn't have it. But Metroid Prime is so sacred to Nintendo fans I imagine Retro/Nintendo were scared to change any more than they had to.
And as for space dragon, I will reiterate, can't we have room for fanservice? You may be clueless, but Metroid fans know exactly who space dragon is and enjoyed that scene for what it is. Again, Retro is deliberately aping Super Metroid with this game, and having space dragon appear in the opening sequence without a backstory is another nod to the classic.
Besides, even without the backstory, here's what you can piece together. Really bad stuff happened on this ship. Bad stuff was clearly done by bad guys. Space dragon must be affiliated with it somehow, ergo space dragon is bad guy. Space dragon flies to planet, implying more bad stuff might be down there. Better go investigate. Is that good enough?
Part of this may be that, as you state, you remember them being very spongey, so now that you know the game and your weapons better and are more efficient, you can defeat them faster - so comparatively it is less spongey. I'd say compared to most other games though it would still qualify as spongey.
But you're right, I don't know the combat as well, so I don't know when to use super missiles, etc. I do try different weapons on different enemies to see what takes them down the fastest, but there are no health bars, so if I can't tell that a super missile is doing a bunch more damage than my other weapons I'm not going to want to deplete a vast amount of my ammo using them. Another area where feedback is important and it's not being provided.
I think I should clarify; I didn't find Omega/Metroid Prime spongey at all. With proper application of your weapons, they went down much faster than I remembered.
Allow me to switch genres for a second and talk about Octopath Traveler. The combat there is a turned based RPG, where you could, in theory, just do the standard attack, attack, attack, heal rotation from the NES or SNES era. But if you do that, the bosses take forever because they are "spongey". OT has a boost/break mechanic that you are encouraged to use to the fullest extent, which dramatically reduces that sponginess.
So is the spongy poor design there? No. If the bosses went down easily to boring attacks, there is no incentive to experiment with the boost/break mechanic and all the other skills that go with it. And there is no satisfaction in coming up with clever strategies. And since attack, attack, attack, heal is boring as heck, it would make combat unsatisfying. In order for the design of combat to be great in this game, the simple approach had to be bad.
Metroid Prime doesn't have nearly as deep of combat as that, but it also encourages you to use your other skills. We don't need a health bar on the enemies (bosses, btw, did have health bar) to learn this; space pirates die in one hit with a super missile.
And again, I want to reiterate. Part of the reward for exploring is to have more health than you know what to do with. Couple that with liberal uses of save stations that refill your health and, well, you can avoid most combat later on when backtracking. Who cares if the pirates take potshots at you? Who cares about running through magma? You'll get the energy back eventually. So yes, combat/platforming can slow down platforming, but it doesn't need to.
Your thoughts on Magmoor make sense for the first time through. If the purpose later on is to be a hub though, the elevators are still too far apart. I just don't enjoy retreading the same rooms repeatedly to get somewhere else. Maybe that's just me though.
I'm not trying to belittle your opinion; people do have different tolerances for this stuff. I feel the game did have a lot of extra connections between different areas, you disagree. I like that the game provided extra optional shortcut routes on the back half of both Chozo Ruins and Phendrana. I think there were more elevators than required. Could they have done more? Could they perhaps have made Magmoor one giant loop or more branches to make it easier to traverse while backtracking? Perhaps. I don't claim the game is perfect. I just don't see it as a problem and think they balanced as well as can be expected.
And I admit I always just thought of Magmoor as that temporary corridor that doesn't count. While playing, I was making a mental note of how often you come back to various areas of the game. Worst case scenario was the landing site at 4 times, but that isn't bad since it includes the very beginning and very end. But I wasn't considering different sections of Magmoor because I always just speed through it.