My favourite
Metroid game is also the
SNES' Super Metroid! I bought
Super Metroid shortly after it was initially released--the first game that I actually saved up for and bought with my own money rather than receiving it as a birthday or Christmas gift--and it felt very much like the previous games upgraded and expanded for the more advanced console. Beyond merely a massive upgrade in graphics and sound: each area in this 16 bit iteration of the Planet Zebes (and the
space lab during the introduction) had a unique, specific character of its own, Samus' arsenal was greatly expanded with new items and abilities, the bosses had the gargantuan gravitas worthy of true bosses as opposed to just being new enemies, and the overall
Metroid mythos felt expanded with a deeper history for Zebes and Samus and a deeper story regarding the relationship between Samus, the last true Metroid, and Mother Brain's pirates.
Super Metroid is in fact my favourite
SNES game, after
Square's Chrono Trigger. I have fond nostalgic memories of a youth arguably misspent exploring the 16 bit iteration of the Planet Zebes, uncovering each-and-every one of its secrets! That game holds a special place in my heart!
However, since the original poster is lumping in the
Castlevania series with the
Metroid series: I must admit that I consider
Symphony of the Night to be an even greater game than even
Super Metroid! (I'll save elaborating upon why I love
Symphony of the Night so very much for that game's own specific thread.)