Actually, I am surprised there isn't a religion for the other alignments.
Lanun would be a prime example of one for a Chaotic Good or Chaotic Neutral alignment religion as they start with Chaos mana from their Capitol. I always felt they were just stuck in there, left with no other civ as a competitor for coastlines, water mana and naval warfare.
There are 2 Dwarven Empires that will compete for Kilmorph. 2 Elven empires that could benefit from the Leaves. Even the White Hand has Doviello that might go for it.
Yea, they can build a Kraken, but who cares? All we have to do is not build naval ships and conquer their cities. Even if they settle on islands for better defense, we can just portal over there and wipe them out.
The Hand seems like a Lawful Evil religion, seeing that the Illians start with law mana and their leaders are Evil.
I read somewhere that Hippus worked with the Illians, yet they don't seem to benefit from snow covered lands. I could see them following a Lawful Neutral Knight code/religion if it existed or the Lawful Good Order. Even a Chaotic Mongolian Genghis Khan style can be envisioned.
On the primary religions:
-The Order is firmly Lawful Good, enforcing its alignment to its adherents, as Junil is not a flexible god and demands unquestioning obedience.
-The Empyrean is Neutral Good, and is less concerned about enforcing its alignment to others as the Order does, adhering to the pursuit of Truth more than anything else.
-Runes of Kilmorph is Lawful Neutral mostly, as they're concerned more about hard work and diligence than being a bulwark against evil, but they still dislike evil.
-Fellowship of Leaves is True Neutral; it only concerns itself about nature and its workings, and only works to protect it and it only.
-Octopus Overlords can be considered Chaotic Neutral/Evil, depending on the sect. Regardless, it's very Chaotic, and because of its nature, Good does not have much room there.
-Council of Esus is Neutral Evil due to its unscrupulousness, but not of the violently malicious kind. Some Aphotic Thrones can be Neutral, however.
-Ashen Veil is just Evil to a T, and can go from Lawful to Chaotic depending on the demon worshiped by its practitioners. Any who dabble in it become Evil, no exceptions.
As for the rest:
-The White Hand is Lawful Evil primarily because Ice is a dogmatic sphere and its adherents want to usher forth a new Age of Ice at the expense of literally everyone else.
-The Dragon Cult is primarily Chaotic, with Good/Evil being decided by the Dragon worshipped; Eurabatres cultings would be Good, while Abashi cultists would be Evil.
-The Children of the One seem True Neutral as they're unconcerned about the games of the petulant children that are the Angels calling themselves Gods, but in the grand scheme of things I'd put them firmly on the Good side.
If you desire more religions, take a look towards the Foxmen, Occis, Stewards of Inequity, and others; Magister expressed interest in having them around as cults due to their relative insignificance compared to the main religions, but adding Cults as its own thing requires DLL work. Maybe if you bug lfgr and he desires to do such a thing, he can add it; no guarantees, though.
BTW, keep in mind adding a Lawful/Chaotic axis on top of the Good/Evil one may require DLL work to be achieved, and would complicate things quite a bit in addition to making this mod stray from vanilla FFH2 and lean closer into Ashes of Erebus, even if very slightly. It's up to Magister and lgfr, really.
Also keep in mind the Palace mana of a civilization tells a lot about a people's personality; The Amurite Palace mana, for example, has Metamagic, Dimensional, and Enchantment, the first signifying their arcane connection, the other 2 an artifact from Kylorin due to their connection with him (Ceridwen taught him sorcery, Nantosuelta trained him even more when he wanted to undo the evil he propagated). The Bannor Law/Life/Fire bundle signifies their passionate struggle to uphold justice, order, and extermination of demonkind. The Illian Ice/Law/Enchantment bundle shows their connection to the sphere and how utterly rigid they are about it, though sadly I can't figure out what Enchantment stands for. Maybe Magister can enlighten us on this.
I am surprised the Clan of Embers doesn't have a Chaotic Neutral Freedom based Religion and a Neutral Animal based one that allows them to create more animal barbarians such as a Panther, Bear and Elephant. Ljosalfar could have a leader that might strive for that one too. Being able to create elephants for use to convert into units, seems like a decent level 3 spell.
Priests of Leaves can create lions, wolves, even elephants at a high enough level via their Call Animal spell already. You can simply go for Fellowship of Leaves and use Priests of Leaves to summon animals as any civilization. There's also Nature's Revolt, which empowers animals to a massive extent.
I do know Orbis and Ashes of Erebus have separated barbarians in 3 groups: animals, savages, and demons. IMO this gives a high level of granularity to the barbarian group, and avoids weird scenarios where Charadon, for example, can have Skeletons go by in peace around him, even though they should be attacking everything as Undead. But again, it's big DLL work, but it's one of the things that are highly worth it IMO.
EDIT: I wonder if the Empyrean/Council can be tweaked to turn Neutral civs Good/Evil respectively, taking from plasmacannon's idea. Maybe a python check when a religion is chosen should do the trick?