Well, for the Organization official one, which ever song plays during the Xigbar battle.
That'd be The 13th Dilemma.
In terms of general music, I'd say The 13th Anthology is the theme where you most clearly can hear out the whole Organization, from the evil Lord Of The Castle to The 13th Dilemma, The 13th Struggle, and The 13th Reflection, back to Organization XIII's main theme. It truly is an anthology: This song is OrgXIII, OrgXIII truly is this song.
But I wouldn't choose it as a battle theme.
As for battle theme, I'd say that heard alone, The 13th Reflection beats the rest of what already is OrgXIII battle music. It has way more depth in it than the other two general battle themes Struggle and Dilemma. And from those two, I'd choose Dilemma over Struggle, because Struggle seems a bit, well, less dangerous and threatening, I guess. However, I'd keep the division of The 13th Reflection and Struggle/Dilemma active... It gives a clear distinction between the old (i.e. Castle Oblivion) OrgXIII members and the new OrgXIII members, which is good, as the two "teams" had different intentions and different styles of deceiving Sora. Of course, for "special" members of OrgXIII, namely Xemnas, Marluxia and Roxas, I'd keep their special themes in place, it makes them stand out from the rest of the OrgXIII crowd, which they ought to.
So in short: keep battle theme the way it is, and replace The 13th Struggle with The 13th Dilemma (or The 13th Reflection for CoM).