Lots of variations. To me, most probable is the remix of their (the individual leader/champion) original theme. 2nd most probable is "each region gets its own specific theme song".Oh yeah with the music there's lots of different routes they could go. For example, you could have the normal battle theme remixed, remix the gym leader theme of B/W OR have a theme for everyone... or just have it based on region, each region gets its own specific theme song, idk, whichever was the e4 theme song of each region maybe?
Or they could make a new theme. Game Freak is unpredictable. I'll just put that out there. Well, correction, Junichi Masuda is unpredictable as he composes and, I assume, is the one who places the music (that piece should go there, that creepy music at the cemetery, etc.)