However, I've always had a problem with the standard D&D/Pathfinder pantheon. The general presumption of most D&D/Pathfinder religions is that a character will choose to worship a single god or goddess out of a large array of deities and only that single god or goddess. This is not how pantheism actually works. The entire point of having a pantheon of deities is to allow the believers pray to and offer sacrifices in the name of any of the deities depending on the current situation and time. For example, a farmer would pray to the God of the Sun so his crops would receive enough sunlight to grow and the Goddess of Nature so his crops remain safe and his harvest be bountiful.
Now, I understand why D&D/Pathfinder favors a more "monotheistic pantheism". Players choose a single deity to worship based on their characters concept and beliefs to further develop said character and the cleric class is built around the concept of an individual dedicating their life and immortal soul to a single god or goddess to gain access to certain abilities and spells. Also, its much easier to worship a single deity instead of a plethora of them.
However, I would gladly trade that simplicity for the interesting stories and conflict that can be derived from a more traditional approach to pantheism. I think it would be a lot more interesting to have a world where people worship multiple gods at once, occasionally offering prayers and sacrifices to "evil" deities when the situation calls for it, making the deities themselves a little more complex and not as black and white.
If you decide to implement this kind of pantheism in your D&D/Pathfinder games, you will need to figure out how you are going to handle clerics. The easiest solution would be to keep the rules the same. While the other classes can worship all the deities at once, clerics have to choose a specific one. They honor the other gods and goddesses, but they only work for one of them. While this works and I'd probably allow this train of thought in my games, I think it would be cool to have "pantheist priests" in the game as well. The only question is, how do you handle that?
One way to handle pantheist priests was presented in Kobold Press' Midgard Campaign Setting. In that setting, the deities are broken up into regional pantheons and a pantheist priest chooses one of these to follow. Every week, they choose two domains from the deities of their chosen pantheon and gain a replacement domain power due to their pantheistic belief. While this would work, I fear players might forget to change their domains every week (I'd probably make it every session to simplify things).
Another way you could handle pantheist priests in the game world would be to have them choose a specific pantheon (whether it be regional or cultural). Afterwords, they would choose two domains from that pantheon's deities that don't contradict each other or their chosen alignment. This choice would make things a lot more simple in some ways, but it doesn't represent the fact that you are devoted to an entire pantheon as well as the first option does.
Personally, I think I would probably use the second choice for its simplicity. Instead of having to switch out domains on a regular basis, you would just choose two and keep those throughout the game. I think its a nice, little compromise between the game rules and the pantheistic worldview. However, that's just my opinion and I can see the appeal of the other option. I might try out both in the future and see which one I like the most.