Well, I have all three, and I can say without any doubt that Emerald is the best. The first and foremost reason for that: Cloning. It makes everything so much easier, as you can clone and preserve pokemon in different stages of their leveling up, you can multiply all of those hard to get TMs, and you can create different versions of/movesets for the same pokemon that you spent so much time and effort in training.
Pokemon wise, you get a much wider selection of pokemon in that version: the 200ish in the Hoenn dex + some Gold/Silver pokemon after you get the national dex. Plus, the hoenn pokemon are just cool: Milotic, Salamence, Metagross, Slaking, etc.
Breeding is much easier, as the magma armor/flame body abilities have a secondary effect, and (if you're into the whole mass hatching thing) its much easier to do because of the Mach bike and the long uninterrupted stretch of land in front of the day care.
If you're into battling in-game, the battle frontier is seemingly endless. FR/LG gets kind of pointless once you've caught Mewtwo, as the battle "tower" is really lame in those versions. I have over 250 hours on emerald, and considering i beat the elite four somewhere at hour 30, I think thats saying something.
Some people think that training is better in FR/LG because of Elite Four round two. I say thats wrong. EV Training is WAAAY easier in the Hoenn region, and once you're done, you can clone rare candies and have your pokemon at level 100 in no time.
If you want those cool Kanto pokemon (Eevee, Snorlax, Dragonite, etc..), well...get both, lol.
My vote: Emerald.
