to avoid repetitions to playable factions, ram gods/ Set's cult centres will mostly be avoided, and replaced by nearby towns' mascots.

faction's name [historical patron god]: emblem or reason
Nile east bank first, north to south

Buto [Wadjet]:
uraeus
Wadjet's name means 'the green one', hence uraeus is recoloured to green, red background for her association with red crown

Per Amun [Amun]:
ram (unchanged)

Pi-Ramesses [Set]:
using phoenix as Ramesses II associated himself with Ra.

Hardai (Anubis):
occupied by Seti in-game so remains as Set Animal.

Uba-Duat [???]:
Apep snake, Uba-Duat is probably a made-up town, since Apep resides in Duat and UbaDuat is Seti's first enemy, i use Apep snake to continue the Set-Apep rivalry

Khent-Min [Min]:
eh Min's symbol could be nsfw;
nearby town Qau's patron god is Antaeus, a combined form of Set & Horus (which could symbolise unification), Serpopard might also relate to unification, hence Serpopard crest.

Waset [Amun]:
too many rams already, and because Nekheb is close to Waset & in-game Waset holds the white crown, Nekhbet's Vulture.

Saww [???]:
couldn't find much info of its religious, Khepri is god of rising sun while Saww is the most eastern faction, Khepri's beatle.

Nubt (Kom Ombo) [Sobek]:
not to be confused with the other Nubt (Naqada, Set's historical cult centre).
Sobek croc on red (Set's colour) background, combining both Sobek & Set's aspects.

West Bank

Rhacotis [Ra]
bennu phoenix

Shedyt [Sobek]
croc

Het-nesut
unchanged, looks like default crest is part of the hieroglyphical name.

Khemenu [Thoth]
ape

Zawty [Anubis & Wepwawet]
jackal

Abdju [Osiris]
Atef crown

Mes [???]
ankh

Kurkur [???]
scorpion

Miam
hippo; Miam is the most northern faction in Nubia; its northern border lies Swenett, named after Taweret.


Main Factions:

Mennefer [Ptah]:
Djed, recoloured to green to fit Merneptah & Ptah

Amenmesse [Amun]:
since Amun is associated with blue,
& the default red conflicts against the red crown of northern egypt,
so Amenmesse is now blue;
secondary colour is white to associate his temporary kingship of Southern Egypt (white crown).

Seti [Set]:
although Set is associated to red, Seti has to share Set with Setnakhte.
Purple, Set animal is recoloured to red, to colour matches Seti' cape.

Tausret:
violet, with green as secondary colour.
we got other main factions with green primary colour, Merneptah & Bay. she's closer to Seti (purple) than Merneptah/ Bay (green) anyway.

Ramesses [Ra]:
gold, with blue as secondary colour.
amenmesses is now blue as primary colour,
also blue is the opposite of red (setnakhte),
so i downplay blue a bit,
shift Ramesses' primary colour to his armour colour, gold.
gold with blue is a pharonic colour as well.

Setnakhte [Set]:
Red, with gold as secondary colour (secondary colour links to new Ramesses)
logo is Was-Sceptre, another symbol of Set.

suggestions are welcomed :)