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?
Holon
The Primal Dialga theme is definitely my #1 Pokemon theme (and video game theme) of all time.