Howdy Center-of-All!
Center-of-All said:
Thing is, the Greek and Roman gods aren't just the same figures renamed. The Romans just associated their deitys with the Greek ones to lend themselves credibility. Mars has a very different personality than Ares, notably lacking the cowardice and bloodlust of the latter, being a model roman soldier. Jupiter didn't have Zeus' characteristic lecherousness, and Juno had none of Hera's jealousy or nagging qualities.
So basically (it sounds like what you're saying is) you could handle the Roman counterparts of all three by using the same stats and simply reversing their alignments.
As a whole, the Greek gods were more interesting, but they were definately different enough to not be the same pantheon, nor do the Roman gods fit the 'evil doppelganger' paradigm (Vesta, most notably, was not any more malicious than Hestia).
If they are originally neutral then they'd be neutral in the other pantheon too.
And what about gods like Janus or Quirinus, who have no opposite counterpart?
Janus I'll be using in a non-Roman capacity as one of the Inevitables. I don't like Immortals of Time. I think Time should be above immortals.
As for Quirinus...here follows a list of Minor Roman Gods...don't expect to see (stats for) any of them (other than perhaps on a list of quasi-deities/demi-deities) in the Immortals Index...though one or two are likely to show up in Gods & Monsters.
http://www.unrv.com/culture/minor-roman-god-list.php
As for the divisions you mention, yes you can see them that way, but the same goes for the various european/near-eastern pantheons. Demeter is really just a variation on Isis, Aphrodite is Innana/Ishtar, Thor bears a striking resemblance to Heracles, etc. This sort of conflation is possible with almost any cultures that share a similar geographical area.
The difference being that all those gods mentioned have their own legends and are clearly distinctive enough to warrant their own entry/stats. Heracles doesn't have different legends than Hercules. Mars may have been held in higher esteem by soldiers than Ares, but there simply isn't enough to make a distinction worthy of a full new suite of stats.
It's just the relative obscurity of these religions that tends to give this sort of impression. People think of subsaharic Africa as a single monolithic culture, ignorant of the enormous differences between the ancient Ethiopians and Khoisan Bushmen, and completely unaware that the Haida aren't at all similar to the Iroquois Confederacy. This ignorance extends to their religions, but that's no reason to encourage that in your works.
Its not about ignorance, its simply about creating a feasible Pantheon, which, taken at face value, you can't have with African Mythology because basically every tribe has its own (name for the) Skyfather: Imana, Chuku, Kaang, Leza, Mawu-Leza, Mlungu, Mwezo, Ruhanga, Unkulunkulu, Wele, Zanahary. Thats a quick list of African Creator/Supreme/Sky deities from a five minute search through one of my mythology books. Its also not like you can say all these gods existed and interacted, because there are no legends (as far as my knowledge of African myth go) of gods from one tribe interacting with gods of another tribe.
Theoretically it might be possible to concoct some sort of over-arching African Pantheon from a bunch of tribal Sub-Pantheons, but all the primary deities therein are going to be Creator/Supreme/Sky, which seems compeltely unsatisfactory.
So either you have multiple Pantheons for each tribe. Completely self-defeating. Or, we take the main gods with the best legends and characteristics fulfilling a given role and fashion it into a workable Pantheon.
PS: Persia isn't part of the Middle East
Here is a map of the Middle East as defined by wikipedia. See the biggest country within it, thats Iran. Iran = Persia.
http://en.wikipedia.org/wiki/Middle_East
I'd personally put it closer to the Vedic pantheon. A suitable replacement might be something from pre-Islam Arabia, but that may be difficult to find information on.
Persia is the very definition OF the Middle East. Classically, Persia was the middle of the trade route between Europe (the west) and China (the east).