they're different
It depends on the plans you have for your hack. FR is easier, but if you want stuff like dive, berrys, expanded space (if you need a lot of regions or something)
FR has jpan's hacked engine, which has a lot of features, and it also has the ability to hold more than one world map (so does em, but you'd need to change the game engine and stuff like that, FR you just make your own map and insert it)
if you dont want to use jpan's hacked engine and do everything yourself, emerald has almost twice as much sprites available because of secret base furniture
there are a lot of more features for each game, i might even make a thread on it, those were just the things from the top of my head