There's three things that bothers me about the ZR theme.
1. The odd noises in the beginning.
I know they are meant to simulate static and a crappy communication link, but they fit better in a trailer than in a theme song. Especially since you get hit by them every single time you start the game.
2. The dialog doesn't really fit with a theme song either, so this is really part 1½ on my list
3. The actual song is very nice, but doesn't carry the same epic whoomp as the original theme. The ZR theme is much more of a "oh shat we lost" kinda song. Very good in itself, but I'm heavily biased towards the stock song.
Much of this have been alleviated with the recent change to play the theme musics randomly on game startup. However, I've been having bad luck and getting 8/10 to be the ZR theme. I've even found myself restarting the game until I get the "correct" theme. >.<
As I said before, there's really nothing wrong with the song itself, but the long streak of noise and dialog in the beginning really throws it off.