I struggle to think as to why there was a period of time people hated this game, considering just how good in general this is in most aspects.
This is easily the Metroid game with the best atmosphere and its not even close, thanks to the music, area design and the like, absolutely insane how they pulled it.
While the sub bosses are a crime against nature, the main ones are incredible, and Quadraxis in particular is on a league of its own for boss fights, genuinely insane.
Its not better than Prime 1, but personally I can count the games that are with only 1 hand, and this is more than a worth follow up to that game, which is all that it needed to be.
Absolutely phenomenal experience.