If classes are based on where the powers come from, then I can see a set-up where druids are the ones that get their powers from communing with nature and shaman's the ones who get their powers communing with spirits. In PF, for example, the spirits include Ancestors, Battle, Lore, and Tribe that wouldn't fit with a druid as I see them. While the spell lists may be fairly similar, Animal Companion and Shape Shifting seem mechanically different than having your spirit connection do something. It also feels like what kinds of spirits are out there could vary greatly from campaign world to campaign world and some may not have shamans at all, just like in some being connected to nature grants no magic, or in others there are no outer plains or gods to power clerics.
This feels to me like the reason druids aren't just nature priests. Getting ones powers from a connection to the outer plains and channeling positive and negative energy feels very different from getting power from the world, talking to it, and changing shape.
My solution to the humanoids only have shamans problem would be to start giving the Orcs clerics if their divine casters are getting the power from worshiping Grummush, the lizard folk have druids if they are all about communing with their swamp environs, and maybe some humanoids commonly have shamans if they get their power from communing with their ancestors or tree spirits or fire spirits or whatnot. Or maybe they all have a mix like humans do.