This is so difficult. Every generation has their gems, and I love all of the different styles. RBY is the classic and the standard. GSC was so dark and powerful, and I am a big fan of chiptune music. However, I also really love the GBA's sound engine, and RSEFRLG are great examples of this music at its finest to me. I think that DPPtHGSS all had great music too, and the more realistic sound engine was a step forward even though I love the classics. BWB2W2 had fantastic music as well. I really can't decide.
Edit: I will say that I feel that the updated versions of Gen I and II's music lacks the punch that the originals provided. For example, I love Blue's Champion Battle theme from RB but I think that in B2W2 it really doesn't provide the same effect. It feels weaker by comparison.