Definitely Birth By Sleep. I may not have played the game yet, but after looking at all its features, I'd have to say it's the best:
*Best storyline
*Best gameplay (in my opinion; the customizable commands and getting rid of the MP bar was a good idea)
*Best music (rage awakened, fragments of sorrow)
kh1 had awesome story and gameplay.
khCOM had awesome gameplay too for gba but i guess not everyone likes the card system. i think if it had a mini tutorial on deck editing, it would have been more fun. that and you have to be the strategy type of player too, or a bit of it. Re:COM was good, but right now i trully hate sora's English voice actor, he has that raspy voice and never actually acts. he sounds like he's a girl.
kh2 was all style, but wasnt structured well, the only thing i thought was a major improvement was gummi travel to be more roller coaster like and some of the soundtracks . Story sucked, great idea, but not enough explanation. kh2 fm was bearable
kh358/2 days gameplay was fun and it was good that it did something kh2 lacked, which was expanding org.13 personality, but story could have been better, plus the choice of worlds was not very good. neverland was really unnecessary. nomura could have done better on that. despite that xion is a very likable character, but at the same time she isn't the most favorite one out of all kh characters.
kh coded- i actually can't comment on this one too much but from the looks of it, it was pretty ok. gameplay looked nice, the story wasn't so bad, the only thing i do wish was that the ending wasn't so vague.
kh BBS- i still can't say much about this one either because i hyped for it and still am but dont know 100% everything on it. story was good, gameplay was fun, it wasn't all hack and bash. still some moments could have looked better but it will all depend on international version. I only wish that the endings could have been more emotional.
EDIT:so if anything...i will have to say kh1 for the moment. until i see how good international BBS version is