It really all boils down to presentation. White all the Gym Leader music is awesome in each game, only one really makes it feel like a huge event for any trainer... and that's the Unova Region's.
The fact that it starts off in the traditional manner is nice, but when your Pokemon is about to faint (although in any battle), a much better peril theme kicks in. It's especially daunting in Gym battles and when facing the Elite Four.
But when the Gym Leader is down to their last Pokemon, much in the same manner as Fire Emblem when all enemy units have been defeated on an escape/siege map, a 'Victory is Near' theme kicks in. To me, it really kicks battling in Gyms up a notch, and that's why I feel the Gym Leader music in the Unova Region is the better of the five Generations.
But that doesn't mean I don't like the others; they're all awesome in different ways.