This is my top 20 list.  If you disagree with the list, then feel free make your own in the comments.

20.) Vs. Dialga / Palkia

19.) Palkia's Onslaught!

18.) Vs. Entei

17.) Vs. Lugia

16.) Vs. Suicune

15.) Vs. Raikou

14.) Vs. Giratina

13.) Shadow Lugia Battle

12.) Vs. Ho-Oh

11.) Arceus (same theme appears in all five mains series games)

10.) Vs. Ancient Pokemon

9.) Primal Dialga / Dialga's Fight To The Finish!

8.) Vs. Unova Legendary

7.) Regi Battle

6.) Vs. Reshiram / Zekrom

5.) Vs. Black Kyurem / White Kyurem (the battle themes for both Black Kyurem and White Kyurem are listed as separate, but I have yet to find a difference between the two battle themes)

4.) Xerneas, Yveltal, and Zygarde Battle

3.) Clash with Kyurem!

2.) Deoxys Battle

1.) Battle with Rayquaza

Which of the music that I've listed here is your favorite?