Well first of all, rather than an unoriginal D&D alignment I'd rather see something more akin to Alpha Centuari's social engineering. You knew where each faction was going anyways for the most part, but it made it more flavorful. You might have choices of the type of government, religion, values, ethics, or attitudes towards implementing a magical society.
As for factions I play I alternate. My first game is generally always Tarth with unmodified Lady Irane. Then I go Gilden or Pariden with unaltered sovs. I usually end up playing Tarth or Pariden with a custom sov because I like those races but their sovereigns need work. I've made a lot of comments in the beta forums previously comparing them.
Tarth should get a bonus to all warfare research because of their gladiator history. Pariden should get a bonus to magic research and the Ironeers should get a bonus to civics research. Tarth needs a much better starting tech and their Sovereign should not be gimped with a rather useless (for an Archer) Tarthan trait for a sovereign trait. The Tarthans I feel should be a bunch of Pseudo-Anarchist-Libertarians who are about united survival and don't have time for good/evil or law and chaos. Their Gladiator history should give them exotic weapons to develop, but they're not so good in groups and don't have large group tactics and are unable to develop the logistical support needed for large fighting groups. They should rely more on Champions and small units. Victory through questing, military or diplomacy but definitely not magic. They would probably oppose anyone who appears to be working towards the Spell of Making. Seanw3 feedback thread has a lot of other great ideas for Tarth.
The Ironeers are Empire builders and believe in the power of technology and a united society. Strong men with heavy armor and heavy melee weapons. Armored Knights in Fortified Castles. I see them not being as good with magical equipment and their enchantments come from spells and not crystal. No magic staves and a weakened spell resistance I could see as being major downsides. They are big on economy, signing trade treaties with anyone they can. Low taxation might be disabled for them. I see them to tend towards turtling and working towards a diplomacy, quest, or magic victory.
Procipinee is on a good start with her crown and the new summoner changes. They should focus on magic and the Spell of Making but be willing to go for a diplomatic victory if possible. By the way, why is it warfare needs civic techs but you don't need to know how to make axes to make magic axes? Anyways more summons for Procipinee is great and more Champions coming to serve her (Maybe a starter quest that gives a champion as a reward?). Procipinee should be a heavy supporter for all her Champions and armies. I also see her enchanting her cities to be more productive. Best mage schools in the land and their best army units should be mage staff casters. Any diplomacy favoring magic development would be golden for her. Special spells might be additional summons or low to no upkeep cost enchantments (No cost enchantments should be limited in the number you can have active). A spell to turn death shards into life shards would be good. Also, she might need a way to generate crystal resources as they are somewhat rare.