Chocobo Breeder to allow for different colors and sizes of chocobos. I don't think they should have any advantages over current chocobos, but maybe have the different colors level the different choco skill trees faster? Like, white levels Healer faster, black levels Defender faster and red levels Attacker faster.

Have a combo class for Botanist and Miner be something Archeologist or Paleontology related where you would gather bits of old civilizations for new recipes for other craters and items for housing.

Chemist that takes alchemy and botany that creates mixtures for use in battle like bombs and salves that share a timer with potions

Or maybe they could just introduce specialization to existing crafts that allow people to specialize in different aspects of their craft. Like Carpenter that specializes in furniture, or weapons, Blacksmith that specializes in different types of weapons, Armorsmith that specializes in different types of armor (or BSM/ ARM could have new high level materials that would require you to specialize in to craft), etc...