Cannot begin to express my love for the second-gen soundtrack. All in all it was just outstanding.
New Bark Town's theme was so good, I almost didn't want to leave. All the other cities' themes were just.. awesome (Azalea/Blackthorn would be my favourite city theme, followed by Ecruteak/Cianwood). The routes were great.
AND THE BATTLES.
Needless to say, I like the Red/Lance/Silver (finale) theme the most, it remains the most badass battle theme to this day. I also really like the Kanto Gym leader battle theme, but I kinda wish they didn't make it as minor-y, I think keeping it major like the original version would have been even better.
With that said, I think Gen I's music is pretty darn great, but overall the Gym Leader battle is the best, and the rest are.. fine. :)