FFIII, job system, multiple airships, submarine, the music, Mini/Toad being useful outside of battles and being used to enter towns/dungeons I thought was a neat quirk. Also loved the DS remake, and the PSP port, which removed the MogNet crap, plus option to use the Famicom version OST.
If there was no III, I'd say II. But I'm one who loved the leveling system, and it serving as the basis for the SaGa games. That and it's more story driven.
Currently playing: Tales of Xillia, Shin Megami Tensei IV, Final Fantasy III, Bioshock Infinite, Tales of Graces f -Dragon Quest is the best
I havent played the originals but judging on the psp remakes of 1 and 2, plus the ds remake of 3, id have to say 2. i loved how the games leveling worked, and it was so fun going to mysidia the moment i got minwu. really helped to level him up for the soul of rebirth, and joseph too
GT:gamingrat91 Final Fantasy IV is the best in the series