I feel the same way about the anime art style that you do the Konami's Best cover. Just kidding.
When I re-bought the game, sure enough, the Konami's Best cover.. But, the case never really left the shelf. I don't display my game boxes, and don't know anyone that does (outside of limited edition/collector's cases that are too big for the shelf) except.. stores. They could put Meatspin on the box and I wouldn't care, doesn't make the game any less great.
The only thing that bothered me about the move to DS from GBA was the art style. Not a fan of the anime look they gave everyone. But even still, outside of the text boxes with the person's picture on it, the art didn't affect the game either. A gem, and worth every dime, no matter how much it is.
My only complaint about the series is how it's sort of left unfinished with the new canon. I love IGA's rendition of Castlevania. If they made it darker, with more innocent people being turned into vampires a la Annette in Dracula X Chronicles, I'd be like, "UH OOOOOOOH!!!!" You know what I mean?
I just wish Julius would hook up with Yoko, and I want want to know what happens to Soma.