I think FRLG are the better games, balance-wise. The gameplay in Hoenn is not that good to me, heavily biased towards Mudkip. Meanwhile, in FRLG Charmander has the poorest matchup against gyms, but he's still very much usable thanks to the options they give you in terms of Pokémon.
Also, Team Rocket is cooler than Aqua/Magma.
Both have some oversights, though. In FRLG, Giovanni's last Pokémon is a Rhyhorn, while it was a Rhydon in the originals. In Emerald, May uses a Torkoal in the second fight, then changes to Slugma the next time you fight her.