I was fully in love with CV64 when that came out, so I was definitely excited for and pleased with LOD when it arrived. Not sure if you're aware, but it was actually being called Castlevania: Special Edition until I believe just a couple months before it was released.
And I still love both games. There are actually a good deal of things LOD doesn't have that are in CV64. Such as: voiceover narration for Reinhardt/Carrie's intro, Dracula speaking when you first run into him in Reinhardt/Carrie's mission (the audio is removed in LOD, and you just have the text), the first level of CV64 is completely revamped/redone for LOD (and it's been a few years since I've played both games back to back, but I seem to recall other level layout/design differences as well), and the special alternate outfits in CV64 are missing in LOD (Reinhardt in traditional Belmont armor, Carrie in a dress akin to Maria's in Rondo of Blood—and when you slide, you can see she's wearing white cotton panties!), and other little details like that.
I agree that LOD should have been what was released originally, but I'm also intrigued by having two different games and spotting the differences. Now if only the N64 could run games in 640x480 resolution much smoother. It feels like such a tease to have the 4MB Expanion Pak option for sharp graphics, but have it be practically worthless because the framerate is so incredibly low. The same things plagues all such games I've played that used the Expansion Pak for higher resolution (Hybrid Heaven, Rayman 2: The Great Escape, and I believe Perfect Dark had the option to use it in that manner in addition to being necessary for the single player mode).
Actually, I believe Quake II used the Expansion Pak for higher res and richer color and lighting (it's one of the most technically proficient N64 games I've seen), and it runs quite smoothly. So I guess it depends on how well the programmers utilize it.
I'm rambling.