Not really.
Zero Mission and Dawn of Sorrow are both better in some ways. So is Portrait of Ruin, for that matter. Actually, Metroid Prime (especially the Wii version) is legitimately better if you don't mind the 3D thing. In fact, just in general "other Metroids and Castlevanias" come at least sorta close consistently.
Other Metroidvania games that I really enjoyed:
Aquaria for the PC. Underwater Metroidvania, but somehow still involves platforming, sort of. The story's dumb, but the atmosphere is great.
Monster Tale for the DS. It's a kid's game so expect it to be easy, atmosphere is also kind of lacking, but the combat is really, really fun.
The Divide: Enemies Within for the PS1. This is basically Super Metroid in third-person 3D. The controls are baaaad but you can get used to them. Heavy emphasis on platforming.
Kirby & the Amazing Mirror for the GBA. ...It's a Kirby game in Metroid format, that probably sums it up. Instead of collecting power-ups, you can go places if you have the right power, which doesn't work as well as the alternative but is neat, at least.
(Also Fusion has tons of atmosphere so you're just nuts.)
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"The courtroom is the garden of holy judgment. Those with lechery in their hearts should leave this sanctuary at once!" ~Franziska von Karma