Also, can you tie certain buildings to different gods? Each god having a different wonder would be pretty cool
I wasn't planning on adding god-specific Wonders, because there'd just have to be so MANY of them. Even if I only limited it to the MAJOR gods, that's still six pantheons, 4 major gods apiece. And since I want to make the 24 choices exclusive (so that if you pick Zeus as your primary deity, no one else can, although if they pick, say, Poseidon then they'd still be able to take Zeus as a minor god), there wouldn't be much point in a world wonder for him. But each god will still have some unique benefit for his/her/its/their followers. (Yes, the tenses get strange; Ometeotl (Aztec) is a dual deity, and Anunna (Sumerian) is a set of 7 beings, I think.) If Zeus is your primary deity and you get him up to level 4 (only possible once you reach Monotheism), you'll gain the ability to have him throw lightning bolts at your enemies (i.e., an orbital weapon in the Classical era!), and the other gods will have a similar benefit.
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Now, I said yesterday that I'd give an example to explain what I'm planning for the god system, and your question gives me an excuse to be a bit wordier than normal. (Be afraid. Be very afraid.)
So you decide you want to use the Greek Pantheon, which gets the most benefit from Priest specialists and a moderate amount from temples. (The active player, i.e. you, always gets first dibs on which pantheon and god to take.) Your four choices for primary god are:
Zeus: Air / Justice
Poseidon: Water / Earth
Hades: Death / Wealth
Hephaestus: Crafts / Fire
You decide to go with Hephaestus. The Crafts focus improves production in all of your cities at the expense of a bit of growth and culture output, while the Fire focus boosts your soldiers, so he's a pretty strong choice for a militaristic player. The game will automatically place a Church of Crafts (level 2) and a Shrine of Fire (level 1) in all of your cities, while your capital will get a special building (name to be determined) denoting him as your primary god and giving certain empire-wide bonuses.
This choice means that you'll never be able to get the Justice, Earth, or Wealth foci, as adding Zeus and company as minor gods only gives you their primary focus. Also, the Greek pantheon lacks gods for Healing, Darkness, Storms, and Balance, so you can't get those foci either. That leaves at most 12 foci available to be added through minor gods, and probably half of those will never really be possible to get. So now we go to the Mandala, the image I'd attached on Friday.
Crafts is a Lawful focus, while Fire is Chaotic-Ephemeral (I keep going back and forth on the Air-vs-Fire issue, but it's CE for now). So on the Mandala, Hephaestus would start at +2 Lawful, -1 Material (+3L from Crafts, -1L and -1M from Fire). That's still fairly close to the middle, which means a large number of the weak and moderate foci (but none of the big ones) will be available.
You play for a little while, and generate enough Favor to expand your pantheon (first minor god is cheap, but the costs scale up quickly, like with policies). Your choices at that point are Hades (Death), Ares (War), Plants (Dionysus), and Knowledge (Athena). Yes, Hades; you can add him as a minor god, solely handling Death without his other Wealth focus and never being able to unlock the most powerful Death-related effects. Darkness and Balance would be available at that point on the Mandala, but the Greeks don't have gods for those (they're a bit biased towards the outer areas), and Justice would be available but that's Zeus' secondary and so is off-limits.
You pick Athena, whose Knowledge focus makes Libraries generate 1 Favor; as your relations with her grow to level 2 you'll be warned when someone else is close to completing a Wonder and your units see further, and at level 3 (which you might not ever reach) she makes Priest specialists in your empire add beakers to your research. Every city immediately gets a Shrine of Knowledge. Since Knowledge is a Lawful focus, adding Athena also shifts you one point in that direction, to (+3,-1).
Next, an event comes up that asks you what you want to do about a Minotaur terrorizing the countryside. You pick the Lawful option and kill the thing to protect the peasants, instead of, say, keeping it around to keep things interesting (C), domesticating it for use in labor (M), or ignoring it to focus on more important matters (E). This choice makes you more popular with the citizenry (adding a permanent +1 Happiness), but more importantly it moves you +1 on the Lawful axis. Now you're at (+4,-1).
Some time goes by, and you unlock a few religious techs (Mysticism, Spirituality, Deism). In your core cities, most of your level 2 Churches of Crafts upgrade to Cathedrals, and some of your Shrines of Fire upgrade to Churches. In a couple cases, your Shrines of Knowledge upgrade to Churches as well. (Favor is sort of like Culture. There's a local effect of upgrading religious buildings, analogous to the border expansions, and a separate global effect of expanding your pantheon, analogous to the Policy gains for culture.)
Again, you build up enough Favor to expand the pantheon. But now your choices have changed a bit thanks to your recent bit of lawfulness: Ares and Hades are no longer options, as you've moved out of the region their foci cover (although you can get back to them fairly easily if you pick a non-Lawful option in the next event). But you've moved far enough into the LE quadrant to unlock Zeus' Air focus as an option, so you go with that; initially he gives a ranged combat boost to all of your Archers, but if you ever get him to level 3 he'll give your archers +1 range, extremely useful in that era. Air is LE, so adding him has a 50% chance of moving you +1L, and a 50% chance of moving you 1 point in the Ephemeral direction. The die roll says E, so you're now at (+4,-2)
You research Polytheism, and those Shrines of Knowledge and Air rapidly upgrade to Churches, giving much better benefits, although this increase comes at the expense of your Fire shrines' growth. It's a good time for you.
A new event comes up, with a lost ship from the Trojan War landing on your shores. Instead of giving them good directions (L), bad directions (C), or making them a home in your empire (M), you just ignore them (E). That moves you to +4,-3.
Again, your pantheon expands. Thankfully, you've moved into one of the 9 "sweet spots" on the mandala (the ones in pink), where 8 or more choices lay. Your options there are Crafts (which you started with), Beauty, Plants, Knowledge (already have), Air (already have), Darkness (can't take), Balance (can't take), and Justice (can't take). So it's a choice between Aphrodite and Dionysus, and you go with Aphrodite for the Happiness benefits of the Beauty domain. Adding her moves you another point towards E, to (+4,-4).
Now you reach Monotheism, focusing on Hephaestus at the expense of the minor gods. All of those Cathedrals and Churches of Knowledge, Air, and Beauty start to downgrade to mere Shrines, although your Crafts and Fire buildings quickly upgrade to impressive Basilica and Cathedrals. It's getting a bit harder to stay religious; while it's great to have practically invincible soldiers backed by giant iron golems, and massive production from your primary god, those minor gods are costing you more than they provide. Also, the growth, research, and culture costs of worshipping Hephaestus are starting to add up, and you're getting left behind technologically. You start considering dumping the whole lot of them and becoming an "enlightened" society.
A few more events happen, and the next time you're offered a minor god to add, the choices are pretty pathetic (Dionysus and maybe Apollo). These are clearly not worth the drawbacks at this point, so you decide to leave the Dark Ages behind. All of the religious buildings in your empire downgrade one level each turn, with Shrines being removed entirely, your mythological units begin to disappear (but refund you part of their cost in research) and after three or four turns you've left the religious age behind (except maybe for a bit of ritual theology if you go for Piety), and your society advances quickly into an enlightened age.
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There you have it. Because you'll generally run out of choices once you get to 5 or 6 gods, I'm going to have the AI suggest the outcome of each event that would put you in the best position to add more gods. That'll be the path the AI will generally take at each event, although I'll throw a bit of randomness in. If you ever reach a point where there are no choices available, I'm planning on triggering an Enlightenment automatically, although that might change.