I have yet to make a final decision. I'll experiment for a few weeks and then decide. This would be a lot easier to do on Ruby if I simply decided to use Hoenn music, but I strongly believe that a Kanto game should have Kanto music.
EDIT: Since AdvanceMap doesn't support 32mb roms properly, here's what I'm going to do if I decide to use Emerald:
Similar to was JPAN did in his hacked FireRed engine, I'm going to blank all the scripts (except the Battle Frontier), and maybe even all the maps too (except Battle Frontier). Then I'll change my rom's header to VILT or something like that, and then I'll create a new entry in AdvanceMap's ini due to me blanking most of the maps & scripts.