well owning both R2 for the Pocket and Neo Blood ex for the Gameboy advanced I will say I enjoy R2 better.
Maybe I am a bit biased, However in Playing the GBA version all I would notice is missing frames here, the timing and button differences, also how easy it was to get through. It looks a lot better graphicaly but with the missing frames and lack of Gameplay I still like R2 better. R@ seems more like a handheld fighter. Neo Blood seems like they were trying to crame KOF 99 on a handheld and were unable to.
I will say though the Special edition GBA is pretty cool. not that it is anything other then a black GBA with KOF graphics. But it is cool being a Neo Geo/SNK Fan to own.