Thinking of the final areas in particular, one thing that exacerbates the limited enemy variety is the way the encounters are paced - you end up fighting the same enemies in the same density to some extent throughout each area of the game. The monotony it creates could easily be broken up by varying things in simple ways - keeping the passages between the baby Metroid's egg hatching and the surface devoid of enemies would have created a tangible difference, for example - a dip between the climaxes of the Queen's defeat and the final departure; instead of dropping you right back into the same gameplay loop of clearing rooms of the same enemies which you were doing right beforehand.
The way they handled the
before the Queen did work well in that regard, but the unwillingness to considerably vary the pace of standard gameplay shows in the way that common enemy formations were pushed up until the moment it started.
That also kind of carried over into the sound design - the reuse of a common cavern theme when you get off the elevator into the rooms before Area 8 proper undercuts some of the gravity of the situation, and would be better-suited to silence. Similarly, if they didn't want to include the droning track that originally played before confronting the Queen, cutting out the background music when
would produce a similar effect.
The way they handled the
larval metroid sequence
That also kind of carried over into the sound design - the reuse of a common cavern theme when you get off the elevator into the rooms before Area 8 proper undercuts some of the gravity of the situation, and would be better-suited to silence. Similarly, if they didn't want to include the droning track that originally played before confronting the Queen, cutting out the background music when
she roars upon the last newly-hatched Metroid's defeat