Ah, the Prime 1 vs. Prime 2 debate. A classic. I can't not go with the original Prime, despite having them pretty close on replays, and that's purely based on how different my impressions of my first playthrough were.
My first playthrough of Prime - which was the first Metroid game I played through (after grabbing MPT on Wii U for $10, what a steal) - saw me immediately play through the game again on a higher difficulty going for 100% instead of jumping into 2. I loved it that much, and was admittedly caught off-guard by clearing the game saving the file and making me replay it to get the rest of the collectables. That gameplay loop of getting lost in a world, exploring every bit just to figure out where to go, getting a new power-up that recontextualized the way I could move around the map, and eventually having my new options narrow down until I was lost again was so good.
Unfortunately, I can't be quite as kind to Prime 2, and not for the reasons you usually see. I took no issue with the more difficult encounters and general hostility of Dark Aether. Rather, my problem is with how the critical path was structured. Prime 1 teaches you rather early that when it comes to progression, the entire map is fair game; it feels like you 'clear' the Chozo Ruins at one point, but then you spend 2 seconds in Magmor Caverns and 5 minutes in Phendrana Drifts before getting looped back to the overworld, and then the rest of the game is spent doubling back everywhere and it's obvious that 'clearing' an area isn't really a thing. Progression in Prime 2 feels more defined; you're given a task of collecting energy from 3 areas, and each area is more or less the same deal in how they're gated. Without sequence breaking, getting energy from one area is what takes you to the next. There are only two points in the game before the key hunt that involve back tracking to a previous area.
Which was precisely my problem. When I hit these points - especially the first one - I wandered around the current area for hours, as I figured chances were I missed something; that was always the case earlier in the game, and the first backtracking point doesn't come until you're almost halfway through the game. It's done naturally; unlike Prime 1, you're not looped back to an elevator (that a lot of the time is also a new shortcut). You just get an upgrade, and the only way to make further story progress is to go back the way you came all the way to the overworld (or, in the case of the second time, back to the second area). It doesn't fit in with the way the rest of the game is structured at all imo, and feels like it was done out of obligation of being a Metroid game instead of something that made sense to do. I eventually just looked up where I was supposed to go (which I never do; I immediately turned the hint system off and forgot it existed, which is why I had to look it up lol) and was just left frustrated wondering how I was supposed to think of what the game wanted.
Now, on replay, that's not a big deal, and I've enjoyed the game a lot. But my first playthroughs of Metroid games are usually the most magical, and Prime 2 had those two spots dragging it down big time for me.