Best story? Eh, I'll say it ties with 2 and 3!
Best bosses? I prefer 3's, but fair enough.
Best voice acting? Definitely.
Best cast? Yes.
Best theme song? No, 2. Soundtrack goes to either 2, 3 or 4, too.
Atmosphere? Yes.
Overall, I'd take 2 and 3 over it.
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Praise the Black Turtle, Game of the Decade Guru Champ.
(Well, I never promised creativity, did I?!)