Sequence breaking is cool because you break the sequences of the item gating. Without the item gating there would be no sequences to break.
I'm not sure you understand what I'm suggesting. Let's take a look at BotW. The shrines, some of which are extremely linear in design, can be partially or outright skipped by clever use of the very tools meant to solve the puzzles blocking the way. That is exactly the same as any other sequence break except the ability and freedom to do so was planned, but the method of exploitation completely left up to the player. What I'm saying is the prime series needs to drop the 'puzzles' that are 'scan the item to see if you can blow it up or not'. There's no flexibility there. Sometimes you can jump over it, or get around it somehow, but that's not part of the design. Make this part of the design and it becomes much more interesting.
And Dark Souls has no sequence breaking whatsoever. It has different paths to go on and cool shortcuts/looping leveldesign, but not a single bit of sequence breaking (running through all enemy encounters to get a weapon etc. isn't sequence breaking.)
I only bring up Dark Souls as it has a similar interconnected world structure to Metroid Prime, however the difference in Dark Souls is that you can take whatever path you want as long as you're skilled enough to take it on. Apply puzzles to this and it becomes a good start of how I imagine a more open Metroid.
Items never were exclusively keys, at least most of them had purposes in traversal and combat alike. The great thing about Metroid is finding the Spiderball halfway through the game and going back to some earlier part and use it on a rail you saw there 5 hours ago.
It's less about the keys and more about the doors. Like I said, there's too many "you need missiles to open this", rather than, "I can probably use missiles here to knock a thing into another thing that opens the door."
Items never were exclusively keys, at least most of them had purposes in traversal and combat alike. The great thing about Metroid is finding the Spiderball halfway through the game and going back to some earlier part and use it on a rail you saw there 5 hours ago.
Could they do more than energy and missile tanks waitng there for you? Of course. Often they do, namely open up new parts, which then is labaled as a key and gating by some people here. Should they stop doing that kind of stuff alltogether? Fuck no.
See, something like the spiderball could be much more interesting than it is. There are a few good rail segments, but what if it did more than just attaching to rails. What if it could grip any surface for a short amount of time? Not only can you use that ability in rail puzzles, but you can combine that with your other abilities to solve completely unrelated puzzles or obstacles.
So, I'm not saying progress should never be impeded, but that players should have more freedom in the way they solve problems. As you said, sequence breaking is cool. And I'm saying it should be embraced.