A small foreword: I imagined these ideas specifically to be used for the re-imagined Vaulters and the Metzari, but nothing prevents them from being utilized for completely new factions. The new factions could be called "Vault Priests" to utilize the re-imagined Vaulter mechanics and "The Golden Templar" for the re-imagined Metzari mechanics, for example. Also the numbers are just examples, I haven't made any calculations about them so there's no reason why I chose those numbers specifically other than that they felt right at the time of writing.

EDIT: this thing grew quite long, apologies for the long read.

I love the fantasy around Vaulters, people who use technology to their advantage and research their ancient artifacts they've forgotten. I always thought that since science is one of the more powerful resources, easily snowballing the game in your favor, a faction that has such a strong boost in science is easily kind of over powered. So I thought that what if they'd need science for more than just research? I call this mechanic I envisioned "Research Projects".

The basic idea is that when you have a city, let's say this would be a Vaulter specific feature, there are several research projects the city can launch. A research project would function much like the stuff you build in your building queue, you pick a project, that project has an associated science cost, and while that project is being completed, it consumes all the science that the city produces. Now since vaulters use a form of arcane tech they don't really completely understand, this feature would work amazingly for them and their existing features. What if Deep Generator instead of just a flat +10% FIDS would give you +5/+5% FIDS (This way it would truly benefit both small and large cities, a static bonus helping smaller cities and the percentile bonus being more useful to the larger ones), but could be upgraded indefinitely with additional +5/+5% increments through research projects, the cost of which would obviously increase progressively? Say you've built a deep generator, but now you've got a chance to have your scientists upgrade its performance, say it costs 500 science to upgrade the Deep Generator to level 2 that would grant +10 and +10% FIDS instead of the +5/+5% of level 1, upgrading to level 3 that produces +15/+15% would cost 1000 science, level 4 that produces +20/+20% would cost 1500 science and so on and so forth. The same could be done with the Strength of the Vault improvement, and perhaps a new improvement "Automated defenses" that adds +25 retaliation damage per turn to the city against siege and an additional "automated defense drone" militia-type unit to the city per level, etcetera etcetera.

Now, simply giving Vaulters more goodies would just make them more powerful, so perhaps we rob the vaulters of their ability to make settlers. The Vaulters can teleport between their cities, but have no obvious tech to do so, so why not imagine they have a piece of machinery called "Vault Core" that is the basis of all their tech and the heart of their cities. So we replace their Settler unit with a "Vault Engineer" that is exactly like a Settler in every way, except that you'll have to build a new individual Vault Core through a Research project for every single Settler you build. This would add powerful flavor to the faction and at the same time restrict their ability to just spam cities and snowball out of control with their massive science output.

Now lets move on to the Metzari. It always bothered me that they were just a reskin of Vaulters, their aesthetics look plenty interesting on their own and I think they'd deserve to be a full faction of their own. Since my previous idea would add a lot of new stuff to the Vaulters, I'd further the thing by taking the Holy Resource mechanism away from them completely and giving it to the Metzari and build that faction around it. A resource being Holy implies a certain degree of religiousness, and the Metzari look pretty warlike, so that would make them some sort of pseudo-religious imperialists, and perhaps purists that don't want to live with other races. Here's a few ideas on how all this could be handled.

First off, the holy resource thing; I don't think that simply treating a strategic resource as a booster makes it feel like "Holy" in the least, Holiness has a certain aspect of permanence to it; you don't change what is holy like you would change socks or like a fashion trend. Thus, I think that your choice in holy resource should be permanent to the degree that it doesn't run out, ever. Changing it obviously needs to be an option because not all resources are available from the beginning, and playing without picking a holy resource until you unlock tier 3 minerals would feel kinda stupid I think. So, there should be a progressive influence cost to changing a Holy resource, and perhaps a 20 turn or so Cooldown on Normal speed. The influence cost could scale with the same things that your Empire plan costs scale with, in addition to being progressively higher for every single time you've changed your holy resource in the past.

Now this holy resource is then used to construct your special improvements, which should be revolving around religion (happiness, influence and security or something along those lines) and Military training. Since these reimagined Metzari would be Imperialistic, the main focus would be on military improvements, both defensive and related to training new units. These improvements could be something like "Inquisitor's Palace" that grants Influence and Security, "Cathedral of Heroism" that grants +100xp for newly trained units and +20 happiness and "Citadel of Faith" that would grant +100 Fortification and +2 Militia units.

As far as how the Metzari military should function, I think they could have slightly cheaper and weaker units than average, but compensate for that by having unique techs that increase their maximum army size. Let's say two additional +2 techs. Their initial unit should be infantry (Legion?), with some sort of knight-type cavalry unit (Paladin?) and a military priest-type support unit (Cleric?) that can heal your own troops. If the equipment of your troops is made out of your chosen Holy material, your troops gain a morale bonus for each such piece of gear they have equipped.

Now the Metzari are an arrogant bunch and have no interest in dealing with the minor factions, thus they would completely lack access to the language square tech, making it impossible for them to parlay with or bribe minor factions. They also would be unable to assimilate or rebuild minor factions. Instead, when they rebuild minor faction villages, they would become Metzari villages instead, permanently, and then function exactly like minor faction villages otherwise. Should the Metzari lose control of an area they have villages in, those villages would now belong to the "Metzari Outcasts" or "Casteless Metzari" minor faction, and they would produce neutral infantry units. They could even be assimilated by other players, perhaps offering some bonus to experience gain per pacified village. The idea is that the Metzari completely slaughter the original population and replace them with their own people. This is obviously an opportunity for someone who conquers the Metzari to gain an assimilation bonus from a minor faction that actually might have a fairly large number of villages.

Other bonuses of the Metzari could revolve around the military/religious aspects; an ability called "Forced Conscription" could allow them to instantly purchase military units with influence instead of Dust, they could have a bunch of military abilities called "Military Edicts" that give an army a temporary buff at the cost of Influence, and perhaps "Civilian Edicts" for their cities. They could also have some sort of small boost to influence, like +1 Influence per district, +2 for level 2 districts or something like that.

I would like to hear your thoughts on the matter.

The way I see it, the Mezari were long ago a race of technologically advanced starfarers. They were part of the Empire, actually. But then one day some of them crash-landed on Auriga. They established a civilization of their own on this strange new world, and integrated themselves with the locals.

The Vaulters are the offspring of these Mezari, and perhaps a splinter-group of the original faction that split off and chose to go underground.

The Forgotten are again a group of people who were once part Vaulters or Mezari factions (not sure which). But for some reason they were banished, and they gathered together to form a faction of their own.

And the Mykara are also connected to the Vaulters. It was a Vaulter (or perhaps some splinter-faction of the Vaulters?) woman who became the leader of the Mykara after her home was destroyed. In their prologue cutscene a structure is shown that has architectural features that looks similiar to that of the Vaulters.

My point is, you should keep in mind that the Vaulters and Mezari still have a lot of space-age technology. And the Mezari especially probably still think a lot like spacefarers, while the Vaulters chose to adopt a more... primitive lifestyle.

But it's all just my own opinion and interpretation of things. I might be slightly wrong or off-course...