This sounds stupid, but the biggest thing that Metroid Prime lacks in is progression. Maybe I should say palpable progression? Let me try to explain.

Frankly, the movement in Metroid Prime blows. The double jump is good, but the rest is pretty middling. One of my favorite parts of these types of games is conquering the map through advanced movement. In Metroid Prime, all you really get is the ability to cross larger gaps. This is good, but I wish it was pushed further. The Boost Ball is also there? Hooray?

Another big aspect of Prime's underwhelming progression are the boss fights. They are so extremely lame it hurts. The designs are so cool I just wish they were 60% shorter and 90% less repetitive and 40% more aggressive. It doesn't feel good to explore, and find mostly combat related upgrades, only for their application to be utterly banal. Why should I care about finding missiles when I know that every time I hit Meta Ridley with one, he'll just go into a canned 20 second flight animation, sometimes multiple times in a row?

Finally, while the map design on a micro level is immaculate in both visual and level design, on a macro level it falls apart quick. Look, the big issue is Magmoor ok? I feel like so much of my time was spent walking back and forth through that same linear part of the map. Admittedly, this could be more due to me being unfamiliar with the optimal routes to pickup upgrades, so this could get better with more playthroughs.

This game has acted as a sort of mental block for me since I finished it last month. Once my life opens up, and I finish the other games I'm currently playing through, I plan on going back and doing a complete new game plus, hard mode playthrough. Consider this a rough draft of my opinions.