Sorry if this comment is too long, I couldn't figure out a way to shorten it. I want to say that your perspective is fine and completely valid. 3D Metroid in a lot of ways can inspire similar debates to 2D Zelda vs 3D Zelda. There's some people that just prefer one to the other. Personally as someone who got into Metroid with Prime, I definitely had some parts of the game knocked down a peg or two for me (the Chozo Ghosts, the color-coded Space Pirates, the weird Sunken Frigate trolling). I'm not really sure where I'd put it in respect to the rest of the franchise these days, but if I could provide some food for thought.
When Metroid Prime came out, the last game in the series was Super Metroid, a game that placed heavy emphasis on exploration and discovery. Super Metroid is definitely in part an "action game", but these elements are so diminished in part because of its admittedly alien controls, its bosses usually being gimmicks or platforming challenges, and a lot of the upgrades in the game straight up undermining the combat. This is the game that Metroid Prime is working off of, not the 20 plus years of 2D games that came after. The 2D games after Super heavily changed the flow of a Metroid game I think, and while none of them necessarily committed to Fusion's linearity in quite the same way, one thing that stayed pretty consistent is a constant supply of power ups, upgrades, and critical paths being overtly obvious. The DNA of Metroid was streamlined into being more of an action romp that features exploration, with a critical path that is usually clearly outlined.
The reason I'm saying this even though you didn't necessarily mention linearity vs exploration or fast paced gameplay vs slower paced gameplay is because in my eyes when you say that you shouldn't have tackled Prime as a 2023 game, I think you're right, but not because it hasn't aged well, but rather just because the franchise isn't the same nowadays. Prime is all about taking that slower pace of Super (at least, slower pace on a casual playthrough) and making that work in 3D. Prime in general is just about playing into the strengths of 3D honestly. It's a slow, ambient, methodical adventure game that uses the time between battles for contemplation and reflection. To me it's not too different from how something like Link riding a horse in Hyrule field is technically a waste of time compared to watching him fly across the screen with a sword, but the ambiance and feeling you get with it is completely different. It's not poorly aged, and I don't think it's really just a "basic" version of Metroid but in 3D either, it's just "different", because the franchise is different.
I will say though I find your take on the amount of areas and the density of them kind of interesting. I don't think I really agree on that front. The amount of areas seems pretty comparable to most Metroid games. Super has 6 areas but it includes its version of Sunken Frigate as one, which Prime doesn't, so it's actually the same amount. Zero Mission has 7 areas but its actually more like 5 because Lower Norfair is considered its own area called "Ridley", and Kraid has his own area. Samus Returns and Fusion for a few reasons are kind of nonsequiturs. Dread definitely has more areas but Dread's areas are pretty disjointed and there's a lot of overlap between area themes (there's like 2 labs except one of them is actually interesting because it's half underwater, there's 2 jungle areas, etc.). I also 100%d Dread for the first time after Prime and honestly, I don't think it's denser either. I was consistently surprised how few upgrades would be in any given tile, and this is keeping in mind the game has the most areas of any Metroid, and even has white tiles that will tell you if there's a hidden upgrade there.
That's just my two cents. I'm not explaining to you why you should enjoy the game more, 2D Metroid is so good that it's only natural to be disappointed when a 3D Metroid doesn't play to your tastes. I'm explaining why the game is the way it is I guess. Sorry if the reasons are already obvious though. I will say about Prime 2 and 3: Don't let the fact that people like them less cloud your judgment of how much progress Prime as a series did or did not make. The thing is that Prime suffers from serious Ocarina syndrome, the first game was so innovative and revolutionary that every game after it was seen as just a worse version, even if each game would play better to different tastes. For example I'm playing through Prime 2 right now and while it's definitely pretty similar to Prime 1, it also is a denser game because of the dark world mechanic, it has better bosses, the combat is better, etc. It makes total sense to me that some people would love Prime 2 or 3 and not 1.