Every person I've seen play the prime trilogy in the past few years seems to like Prime 2 the most of the 3! But for some reason Prime 2 is remembered as the worst of them. I think Metroid Prime 2 was disliked a lot when it first came out because a lot of games were doing a light world/dark world thing at the same (or recent) time. I'm sure there's more to it than that but i remember that coming up a lot.
The difficulty may have been a part of its original mixed reception, since it's a harder game. But Prime Trilogy made it easier, and people are into way more difficult games like the Souls games these days. Also people are probably going in knowing it's a little weird ahead of time, whereas a lot of people who bought it in 2004 probably had different expectations based on it being the sequel to an instant classic. Also Other M showed us how truly bad the series could get and kind of made everyone reevaluate some of the less universally beloved entries in the series
