Very difficult, especially because of the inherrant qualities of the songs.
IMO, red's theme is an excellent final battle, particularly for a pokemon game. It has the sort of "pokemon" feel you tend to look for. Also, to the trolls throwing temper tantrums about 8 bit, 16 bit, w/e, you do realize this same theme exists in HG/SS, and B/W in significantly higher quality, right? Get over yourself.
Cynthia and Iris, though, also have very good themes. However, while they are probably better SONGS than Red's theme, they aren't better CHAMPION songs.
It's akin to arguing the quality difference between Mozart and Queen. Both fantastic music in their own right, but different for entirely different reasons (yes, I'm aware of the scale difference between mozart/queen and pokemon games; please save your buttmoaning for someone else).
That said, I vote red/lance, even though it's not necessarily the better song. It serves better in the role of Champion music, IMO.
I cannot protect you without holding a sword. I cannot embrace you while holding a sword.