i feel the same, but it may be nostalgia. i only played through the entire trilogy in like 2018, way after my first playthrough of the first prime. prime 2 has a very different feel, more like a constructed game world than something that fits together naturally. it's also a lot less colourful and the dark/light thing feels sort of slapped on.
prime 3 is all over the place. i haven't played 4 because i don't want to buy a switch 2.
i think the evolution of the prime series served to have it fall more in line with the original vision for the character of samus aran, which famously is very different in the english-speaking world due to a mistranslation. the word "bounty hunter" should have been translated as "mercenary". if that hadn't happened, metroid prime would probably have been a lot closer to halo.