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
OoE isn't very good. (Pretty sure I didn't even bother to finish the game)
But I know I'm in the minority with that one.
SotN is top notch though
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Never underestimate the power of stupidity in numbers. ~War13104 Never stoop to the level of idiots. They will drag you down and beat you with experience.
I also really enjoyed Bunny Must Die (PC, free), though it's the kind of game I can see some people hating. The controls are rather annoying to get used to, the game practically requires a guide to figure out what you should be doing at one or two points, and the story is intentionally nonsensical, but I still found it really fun overall.
Personally, every 2D Metroidvania-styled Castlevania except for HoD is better than SotN. Of which either Dawn of Sorrow or Order of Ecclesia is the best. Zero Mission is also an excellent Metroidvania that surpasses Super Metroid in a lot of ways.
As for 3D games, all three Metroid Primes (1>3>2 btw) and Dark Souls.
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Something something something ^Poorly disguised anti-caps sig
HoD isn't even the worst Metroidvania in the series!
(CotM so bad)
I will fight you.
Definitely give any of the handheld Castlevanias you haven't yet played (except HoD) a shot. None of them beat SotN's atmosphere, in my opinion, but they all add their own little spin to the formula and are much better balanced in terms of difficulty, which is to say you might actually die if you try to play with your eyes closed.