I have always been of the opinion that pantheons are as tied to the world as the names of its nations and the uniqueness of a game setting. Each world should have a pantheon of its own giving it flair, flavor, and distinctiveness.
When one creates a cleric or a character with a divine-feel, the choice of the deity greatly influence what type of character will result. A cleric dedicated to the god of death as opposed to a god of healing and life usually play very differently. A holy warrior of the god of war or the god of commerce does not have the same outlook on things. Their choice of deity changes how the PC will approach certain situations.
Existing vs. New Pantheon
There is much to be said about reusing a pantheon when creating a new campaign world. First, it allows the creator to use something he and his players know. No need to spend a long time explaining the god represents what. "You reached the temple of Zeus in town." Most players would know that he is god of lightning and royalty. However, he brings with him a lot of baggage and myths you may not want in your world: his constant womanizing may not be something you wish to include in your campaign, or Hera’s jealousy and constant vengeance upon his loves.
Creating a new pantheon is exciting. It is an opportunity to create a unique cosmology for your world. How was the world created? Did the god of the sea and the god of fire wrestle? Did the sky god and the earth goddess fall in love? However you wish to spin it, the gods and the cosmology of the world are tightly woven together.
What are the relations between the gods? How do they interact with each other? Why is there one who rules over them? Is there a head of the gods? Why?
Regional vs. Global Pantheon
I like having a common, core pantheon of a few greater deities who are worshipped pretty much everywhere. Those deities should be few in number: six to twelve are a good number. Other deities would be local and add flavor.
Changing the pantheon when one travels throughout the world is just complex. It forces so much work on the DM/creator and generally confuses the players. Isn’t Abagug the god of fire? Regional pantheons should add a few gods to the overall, and not make the world much more complex. Locally certain deities might appear major, but when one leaves their centers of worship, they are quickly forgotten.
How many Gods are too many?
If there is more than twenty major gods, there are too many for a unique world. Most of the others simply become redundant or lacking in flavor. Local and minor gods can be added in infinite numbers, being limited in influence.
Yes, the Greeks had hundreds of Gods, but of those only twelve were widely worshiped. The "big twelve" were: Zeus, Hera, Poseidon, Athena, Hermes, Apollo, and either: Demeter, Ares, Hephaestus, Aphrodite, Artemis, and Hestia OR Alpheus, Cronus, Rhea and the Charites (the three Graces) (depending on the source). Of those big twelve, each city usually had a patron they worshipped over the others. Thus there were usually two or three main gods worshipped in a given town.
How many Gods are too few?
Obviously, this is a fantasy game and a monotheistic model is not the most interesting thing to have. Similarly limiting a players’ choice to ten or less deities is overly restrictive. I think twenty is a good medium. It allows for variety.
Unclear Pantheon: The "Arcanis" Model
I think Paradigm (creators of Arcanis) first came out with this concept I call the "unclear pantheon". In traditional D&D, a god is given a clear alignment and his church follows that alignement. Any off-the-path cult is usually manipulated or masquerading as worshippers of that god. The unclear pantheon is fuzzier. The gods or their church do not have alignment. A deity can have chaotic, evil, good, lawful or neutral followers. Cults regroup people of a similar mentality (evil people flock to evil cults, good to good, etc). This blurs the line between factions and alignment.
This model is best, I believe for a campaign where the line between good and evil are is not clearly defined and where the PCs must decide on the lesser of two evils.
Portfolio: stick to the important stuff
It is impossible to cover everything when creating a pantheon. The major gods should have defined portfolios that cover whatever is most important in the world. Common themes include the sun, water, family, fertility, fire and death. However in a primeval world, the seasons might be most important.
Don’t try to cover everything. Cover the important things first.
The Forgotten Realms Fiasco
Frankly, I include this one for completeness, but I doubt you will ever see a JP setting with this as a premise. I can often be said that "in Forgotten Realms, the gods play poker and they trade followers, portfolios and influence." That is, gods rise, fall, change folio, all within a ridiculously short time span.
To me, the gods are something that hold the world together and while they can either interact with the world a lot, a little or not at all, who they are and what they represent is mostly immutable. The sun god is the sun god! Not the sun god today, the torture god tomorrow and the god of thieves next week.
Add to that the ridiculous number of deities in Forgotten Realms and you have it. As the title reads: Forgotten Realms fiasco!
Classifying the gods
I think there should be three classifications of god:
Greater A greater god is a deity that is commonly worship throughout the world, or a large portion of it. Finding temples and shrine to this deity is common anywhere. Usually, the church of this deity is powerful and rich, having fortresses and militant orders. Most people can easily identify the symbol of this god. A good example is Pelor in Greyhawk: his followers can be found pretty much anywhere.
Regional A regional god is a deity whose worship is usually limited to a finite geographical area. Regional gods are well-known and their worship might rival that of a greater god in that area. However, beyond that, they are either unknown or with very limited means. An example of this would be Pholtus in Greyhawk: they are extremely powerful in the Pale, but have limited influence outside the theocracy.
Saint or Hero-god A saint or hero god is usually associated with a single location (lake, mountain) or city. The church of the god is limited outside that area. An example of this would be Marduk, the patron-god of the city of Babylon. His influence was initially limited to the city and the land it controlled.
Even after I wrote this, I am not certain of the avenue I wish to take. I like the core and regional pantheons approach, I like the unclear pantheon, I like to categorize the god with their sphere of influence...
This really has not helped. I am still exactly where I was before!