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For me definitely Ruby/Sapphire. First series I started with, and I still remember some of the surfing tunes. Can't remember for the life of me what Black/White music is like.
The series has always had great music. I can't think of any Pokemon game I disliked the soundtrack of.
That said, Gen I + II really had some of the most memorable music in the series. Even though they're chiptunes, the melodies hold up surprisingly well. Gary's champion theme is my current morning alarm :P
Generation three had the best music, in my opinion. Few of my favorites would have to be Elite Four encounter, Regi battle theme, Lilycove City, Fallarbor Town, rival theme, and Magma/Aqua battle theme. Gen six had some great music as well, and so did generation one.
VOTING FOR HOENN hands down. As much as I hated the remixes in FR/LG from all the great chiptunes in gen I Kanto, the melodies and trumpets of Hoenn are still today the best music from any pokémon game imo. Just remember the first time you went into Route 104 and heard the wonderfully adventurous music there... Or when you struggled through the ashes of Route 113 listening to the strangely melodramatic and different tune there... Or when you went through the rain and all those darn Tropiuses and Oddishes around Fortree and heard the two pompous melodies played in those forests... Or when you were outside of Mt Pyre and heard the somehow awesome intro to the music there... Or when you battled Team M/A on top of Mt Chimney... Or when you battled the Team leader... OR WHEN YOU BATTLED STEVEN (Wallace maybe?) at the end, that music was pretty epic. Or the ending theme, that brought tears to my eyes. Not to mention the title screen music. Still today the best title screen tune overall for pokémon games imo. It was just perfect.
Yeah. I loved the Hoenn music. :3
Then there are of course some of my favorite tunes from other regions. Route 10 in Unova, Violet City in Johto, some of the route music Sinnoh and the wonderful Pokémon League theme from Kalos. And the original, 8 bit or something Hall of fame tune from Pokémon Yellow. <3
I honestly can't pick just one generation worth of music as my favorite, as they've all got a few themes that I really like, and they also have a few that I'm kind of 'meh' about.
If I have to choose though, I'd go with Gen II very slightly edging out Gen III, with I and V right behind that. I've always been a sucker for the Game Corner music in the second gen games, and the Ruins of Alph and the Lance/Red theme are two of my favorite tracks as well.
Gen 3's music wins for me, hands down. The Drought, flood, Magma/Aqua leader battle and the Regi battle music were my favorites from it. I also liked some of Gen 5's, which is why I also voted for it.
I have a soft spot for the Gen III music because it's very catchy. I also like the Gen VI music; I even downloaded the whole X/Y soundtrack from iTunes because I liked it a lot.