Castlevania 64 and Legacy of Darkness are really the only three-dimensional Castlevania games I've cared to play through more than once.
SotN is amazing for what it is, but that's almost an entirely different take on the series (for a number of reasons). It's safe to say that Castlevania 64/LoD was the last game that made me feel like it was more about having to drive a wooden stake through the Count's chest cavity at any cost, rather than beautiful anime men, whose powers seem only limited to imagination.
There are no wooden stakes in Castlevania 64/LoD, but I felt limited, vulnerable, as I should. I enjoy all of the titles so far (with the exception of Lords of Shadow), but for different reasons. Konami created a fork in the road over SotN's popularity, and I'm not bitter, but I certainly wouldn't object to more games like Castlevania 64/LoD (three-dimensional or not).