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
just swap the pink color to be the first color of the 16 colors in the palette and whatever color was first, put it where the pink color was at and yes you have to for each. If you have a lot of red tiles like a red chair, red fire hydrant, red house, group them together and usually the 16-bit versions of them come out to look nice enough to use.