I agree with this (though I haven't played Prime 3 yet), but I'd like to say that with Prime 2 it's almost a technicality more than anything. Like there's less areas in the game, so that already takes away a lot of the amount of quality tracks. I would still say Prime 2 has a worse OST than Prime even taken on its own merit, given that tracks like Agon Wastes exist, but I'd say considering most of what you're hearing throughout the game is stuff like Temple Grounds, The Luminoth, Torvus Bog, the Water remix, Sanctuary Fortress, and the Main Menu theme and its fanstasic End Credits remix, it feels a little weird to say people are living off the highs of the soundtrack when on average the great tunes probably account for like 70-80% of your playtime. It's like the reverse Tropical Freeze! Not a lot of variety but tons of time to appreciate the great tracks.
What you're forgetting is the dark world, though. Probably not quite half the game, but you spend a lot of time in the dark world versions of each area, and none of them have memorable music. That plus Agon being essentially 1/3 of the main areas takes a toll, though I'd say it's probably worse towards the beginning when you haven't gotten to Torvus yet and towards the end when you're spending a lot more time in the dark world.
I'll also say that outside the Parasite Queen and the Ridley remix, I can't really think of a great boss battle theme from the first two games. I guess I kind of like the Vs. Dark Troopers?
There are a good amount of solid ones from both, but Parasite Queen is probably the best, yeah. Prime isn't known for its boss themes, but it has them.
Also, apropos of nothing, I think it's neat how big of a leap forward Prime was for Kenji Yamamoto as a composer, you don't often see that. He's always had an issue with being kind of static and straightforward, which is probably the biggest difference between his work and the Hirokazu Tanaka Metroid soundtrack he's imitating the style of. But in Prime he gets an extremely distinctive sound of his own which helps break him away from just copying what someone else established, and the leap in complexity when you put Magmoor next to Phendrana or Torvus Catacombs next to Torvus Bog is really obvious.
I feel like Hollow Knight might be a good example to look at re:Nonlinearity
Where there is still something of a sequence, but the sequence branches in different directions at a certain point; some upgrades are still prerequisites for others, but there are two or three parallel options for what the "next upgrade" is.
So it would be like, if once you have the Spider Ball in Prime 1, you can either go to the Tower Of Light to get the Wavebuster, or to the Chapel Of The Elders for the Ice Beam. But instead of the Wavebuster being a one-off detour, that would in turn be required to unlock another upgrade somehow, (let's just say you need it to give a more sustained charge to something that the normal Wave Beam can't, and behind that gate they added Seeker Missiles or something) so then it would be a choice between following that new sequence, or going for the Ice Beam. And then if you get Ice Beam, the choice is between the Gravity Suit or Seeker Missiles.
Either way, you're still following a sequence and making progress, and eventually you'll need to get them all anyway, but the order of progression isn't so strictly tied to one exact golden path.
So forgive me going off on a ramble for a bit, because I find this subject fascinating:
A decent number of Metroidvanias let you pick which item to get first or let you use either/or to progress, though how explicit that is really depends. Super Metroid and Zero Mission have a clear intended path, but you can depart from it by doing things out of order or skipping certain abilities (for instance you don't actually need the Grapple Beam or the High Jump Boots to finish Super). If you choose to ignore the directions of the Chozo Statues, then you can find that there are many different ways to go about finishing Zero Mission, though the complexity is somewhat lessened by how short and small it is. The choice is really limited to whether you fight Ridley or Kraid first, and what items you have when you do.
Hollow Knight takes more after Symphony of the Night, which opens up a lot of the world at once very quickly. The path to finishing SotN requires very few of the relics, and there's a lopsided balance where many of them open only a few rooms if they do anything important at all, and then Jewel of Open, Leap Stone, and Bat combine to open pretty much the whole map. A lot of older ones worked sort of like this I think, where the item progression wasn't the main thrust of the game and they were rather open, with most items being completely optional upgrades. The first Metroid was a lot like this, get a few key abilities and you can pretty much go wherever.
The big difference between Hollow Knight and SotN though is that you generally still need to acquire specific items in a specific order in SotN, so the map being so open is more or less a giant red herring. You need the Jewel of Open for the Leap Stone, the Leap Stone for the Mist, the Mist for the Bat, and so on. So despite the many ways you
can go, there is only one right way. In Hollow Knight, you can get different abilities that open up different areas, or offer different means of reaching different areas, making progression itself unusually nonlinear. This does eventually break down into a more SotN-like arrangement towards the end if you aren't settling for the bad ending, which comes with the same problem that you need to find a few very specific items in a huge world. Games like Super Metroid ask you to do this regularly, but use a lot of tricks to make it relatively effortless. Two favorites are locking you into a specific section of the map or always putting the next item fairly close to the last one. Since Hollow Knight and SotN are so open though, you really do just have to look absolutely everywhere, which can become exhausting (moreso in the former because it's so damn big and much much harder).
Pseudoregalia is another similar game. After the introductory section, you're set loose and can go to a bunch of different places, and get a bunch of different abilities in pretty much whatever order you like. It's similar to Super Metroid in that most required upgrades are related to movement in some way, and if you're good enough you can often figure out a way of getting somewhere with what you have rather than the intended ability. This can make it quite unclear what "the way you were supposed to go" even is. Unlike Super Metroid, there is no one explicit intended path through the game, just intended item progression gates. It also runs into the issue of what happens when it closes up though. One of the most important upgrades requires you to interpret a cryptic message referring to the naming scheme of three key abilities, and know to come back to this tower if you don't have all of them yet and use them to enter it and get the upgrade and information on your main objective. Unfortunately, it's very easy to miss this, or do what I did and assume the cryptic message
was referring to the main objective. It's not obvious that the tower can be entered at all purely through acrobatics, especially if you immediately peg it (correctly) as the game's Tourian equivalent that you'll need to return to at the end of the game.
It's worth noting though that even if you avoid the pitfall of eventually sending the player looking for a needle in a haystack, you do
lose something from this open approach as well though. It can be hard to tell if you're actually making progress, and a lot of the satisfaction of growth and being able to solve another piece of the world's puzzle is muted compared to the pretty intense feedback loop of get ability -> use ability -> get ability that Metroid provides. Both Hollow Knight and SotN have
far fewer new abilities than a Metroid game does, despite SotN being about the size of Super and Hollow Knight being way larger. It's probably prohibitively difficult to have this kind of structure with such a large number of abilities, since it will increase the complexity further and further for each additional item you add. Most of the abilities themselves are on the simpler side too, there's a reason you see wall jump, double jump, slide, etc. recur so often and usually make up most of a game's selection. Meanwhile Dread has so many different abilities and advanced techniques that it's like playing Celeste with a Zelda game on top of it.
But speaking of The Pitfall, I think it's actually really hard to totally avoid this unless the game never completely lets go and continues to just tell you where to go and give you no options for the whole duration. And the ways in which Metroidvanias attempt to control players are just as interesting to look at as the ways they give freedom, like how Metroid Dread is constantly and blatantly closing paths behind you and trying to funnel you in the direction it wants, even though it is very much still possible to get lost or even sequence break. But even Super Metroid eventually has to take off the training wheels and give you access to the whole map once you get the Power Bombs, or ask you to remember some very distant rooms to enter Lower Norfair and Tourian. It seems like an inherent hazard of being true to the spirit of the genre, you're going to have to compromise with some map markers like Hollow Knight did or something or else just let the process of "check every possible room across the whole map" play out.
The last notable example of open design I'm aware of is Rabi-Ribi, which is kind of different. It has a hidden Super Metroid wall jump available from the beginning along with various other tricks like Zero Mission-esque hidden paths explicitly for the purpose of letting you complete every part of the game in basically any order, and it's probably one of the largest Metroidvanias as well. Normally however, it opens up in "phases", where you are meant to go find and defeat a few specific bosses at a time. The game typically has a loosely suggested order to them, but if you don't mind a rougher experience or even just get lost, it's not too hard to break from these suggestions and do things differently. I think it often deals more explictly in soft locks rather than hard locks. Like, you don't actually
need the Gravity Suit equivalent to explore the underwater area, but it will make it a lot easier. It does a ton of really interesting and original things for the genre including its takes on concepts like difficulty levels and new game+, which is all somewhat obscured by how it looks like a hentai game. The sequel/spiritual successor had a much larger emphasis on plot, and that proved to be mutually exclusive with this, so despite whatever other advancements it had, this stuff had to be confined to an alternate mode I believe. (I can't speak in as much detail on these games because I've never played them personally.)
I've been curious for years to see how exactly Prime 4 will be structured, because the possibilities are kind of fascinatingly endless. The first three games were in some ways built very similarly, but in others completely different. All of them are pretty aggressively linear and actively patch sequence breaking through updates to later editions, even Fusion didn't come off as strongly opposed to it as Prime does. They all have you tackle areas mostly one after another, with you beating the boss of one and moving on to the next, but with 2 or 3 sudden departures sprinkled in where you need to go across the map for one item and then come back to continue.
However, the first game is structured to heavily imitate Super Metroid, and that includes an interconnected world with one "crossroads" area that connects to everywhere else. The second game goes outright for a pretty explicit hub and spokes design. It's probably the most Zelda-like Metroid game for several reasons, not least of which is the two worlds gimmick. Corruption breaks its world up entirely into isolated sections that often aren't even on the same planet, which gives getting around a very different feel since your ship acts as a sort of "fast travel" or a universal elevator between unlocked landing points. You could say there was a trend between each entry to make travel more and more centralized, which I think was necessary to begin with due to the aforementioned "now go to the other side of the map" tendency and for one other reason: unlike 2D Metroid, the upgrades you get in Prime are mostly of really minimal help in backtracking through old rooms. There's no plowing through or flying over everything, or mowing down enemies with increased firepower. Backtracking is a lot more tedious in Prime, so it was in its best interest to make going between areas as streamlined as possible. There's also the key hunt, which is a major factor in all three games, but handled pretty differently in each one.
It's entirely possible with how much Retro Studios has changed over the years that most of these unifying quirks will no longer apply to Prime 4! I don't have a conclusion here. There are so many possibilities that I have no idea what structure I'd like to see. Something I do want is for them to double down on areas that feel like classic 3D Zelda dungeons, which was always my favorite part of Prime and which I think might demand a more linear game, but it's not like I can say for certain. One of the funnier thoughts I've had though is that I wonder if any of Tropical Freeze will bleed into this. Will they design areas with less random machines triggered by morph ball slot and more mechanics specific to the environment? Will movement and flow through rooms become a much bigger focus than before, even to the point of bringing the speedrunning aspect of the series originally excised from Prime back in? Will we get an obscure background cameo of Diddy Kong that takes four years to find?