Tough one, hmm... I prefer the D/P Route music and Legendary battle music, but I like a lot of R/S/E's area themes (such as Towns, Abandoned Ship, Meteor Falls/Cave of Origin, Sealed Chamber) more than those of D/P. Both are good mixtures; I'd have to sit and think about it to get a clear-cut answer, but overall I think I prefer the D/P music.
New battling system (physical/special attack split) or Old battling system (whether an attack is physical or special is determined by the type)