are you talking about the music or the actual fight? because in both cases, the music is extremely appropriate and emotionful toward the situation...
if you're talking about the fight in both films, then yes, the duel of the fates is much more crucial to the story overall. It shows the fall of a hero and the potencial fall of the jedi when obi-wan is told by yoda that he can train anakin.
whereas, the battle of heroes seems very appropriate to explain how vader became the vader we all know and love/hate. but it seems like lucas was like, *gotta think of a way to put him in the suit*. it probably wasn't like that, but it seems (not necessarily last minute but) like lucas didn't think of it being the way vader became armour-clad...
tbh, both fights are extremely powerful and fun to watch...and both give me goosebumps when i watch them...
Choreography wise, DOF beats BOH hands down imo. BOH was far too repetitive for my tastes.
Music wise, i used to prefer DOH, but the BOH music has really been growing on me.
BOH for me is actually kind of poor, up until a point. Up until they land on the lava platform things, i think the fight is just poor. there's no sense of what's truly at stake. there's no "omg anakin really has turned and is fighting his master" feeling, at least not for me. once they hit the platforms, though, everything shifts. even the choreography, where they seem to be dragging the sabers against each other, gives you the impression that both men are physically and emotionally spent. the emotion finally kicks in when obi gives his "you were the chosen one" speech.
up until the lava platforms, though? it sucked, and was saved only by inter-cutting with the yoda battle...
DOF has great music, some really nice choreography, and when jinn goes down, you can see even in the way obi-wan fights that he's more determined than ever...
After listening to them again BOH is definetly better. Sure DOF is great but BOH has some awestriking moments... like at 1:35 and greatesat of all the twisted unholy form of Binary Sunset AKA the FOrce theme at 1:57.
But as I said earlier nothing beats this... from 7:15 to about 8.