There are 17 Minor Factions by default in Endless Legend. Their presence in the game is limited to small settlements called Villages. In every region in the game, there will be at least 1 Minor Faction Village per region, and a maximum of 3.

There are three statuses for the Villages: Hostile, Destroyed, and Pacified.

HOSTILE: all Villages will be hostile towards you by default at the beginning of the game, and eventually spawn enemy units (called 'Roaming Armies') that will, as their name implies, roam around the map and most likely attack your units should they meet them. Rarely, Roaming Armies will even put your cities under Siege.

DESTROYED: you can attack villages and, should you win the encounter, the village will be destroyed and be unable to spawn any more units. This can lead to Pacification if you colonize the region and rebuild the Village through the city's building production menu.

PACIFIED: Pacified Villages add bonuses to any city in the region, namely: 1 additional population per Village on the region's City; +5% Unit Reduction Cost of that Minor Faction's Units per Village; and, finally, the ability to be Assimilated into the Empire (more on that a bit later). Pacifying Villages is the best option (for the free population and Assimilation Perk). Pacification can be achieved 3 ways:
----DESTROY AND REBUILD: attack and destroy the village, colonize the region, and rebuild the Village through the City's building production menu.
----BRIBE: Requires the Technology "Language Square". Pay an amount of Dust (scales with how many Cities you have) to pacify that ONE Village immediately. Gives 6XP when performed with a Hero. If there are more than one Villages in the region, you'll have to Bribe each one individually.
----PARLEY: Requires the Technology "Language Square". The Minor Faction will give you a quest; upon completion of the quest, ALL Villages in the region will be Pacified. Gives 6XP when performed with a Hero. Some of the quests are difficult to finish, and some have time restrictions. If you fail the quest, you can't get another Parley quest from that particular Village--but you can get it from another Village in the region, if there is one. If there isn't another Village in the region, you'll have to Bribe or Destroy the Village to Pacify it.

When a Village has been Pacified in a region you own, you gain the ability to Assimilate the Minor Faction into your empire. Each Minor Faction has a unique perk that, when Assimilated, will apply to your entire empire. The perk scales in effectiveness for each Pacified Village of that Minor Faction in your territory; thus, it's best to try and settle regions with Villages of a Minor Faction you're interested in, and to only Assimilate Minor Factions that you have several villages of (2 at least). Assimilating a Minor Faction will also allow you to build that Minor Faction's units in your Cities (see next section).

You can Assimilate 3 Minor Factions. Only 1 slot is available at first, with more unlocked through Technologies:
Era 2 Technology: Native District
Era 4 Technology: Cultural Indoctrination

A Minor Faction can be Assimilated at any point after you've Pacified one of their Villages on your regions, as long as you have a free Assimilation slot. It costs a moderate amount of Influence to Assimilate a Minor Faction, and the cost scales with how many regions you control. Assimilated Minor Factions can also be swapped out at any point if you find one you like more later (or depending on the current needs of your empire) as long as you have the Influence to do so. Assimilating a different Minor Faction will NOT get rid of any Minor Faction units you have already produced, however they will not be retrofittable any longer.

Choosing to Assimilate Minor Factions that play to your empire's strengths is key. Necrophages, for instance, greatly benefit from the Sisters of Mercy's, Geldirus, or Gauran's perks (because Necrophages are practically always fighting someone) while the Vaulters can get insanely high amounts of Strategic Resources with the Silics or Science with the Haunts. Again, you can swap out Assimilated Minor Factions to suit your empire's current needs (at war? Swap to Ceratan for extra defense on your Units. Exploring? Go for Jotus or Erycis).

The full list of Minor Factions, and their Assimilation Perks (per Village), is listed here. So if you have 3 Villages on your Empire, multiply the perk accordingly (i.e. 0.5 * 3 = 1.5):

In addition to receiving the Minor Faction's perk after Assimilating them, you also gain the ability to design, equip, and produce their units in all of your Cities.

Choosing a Minor Faction whose units complement your empire's current roster is a good idea. The Ardent Mages, for instance, may want to Assimilate a Minor Faction with tanky units like the Urces or Silics (since most of the Ardent Mage's units are squishy). Major Factions without a Flying unit in their roster may want to Assimilate the Haunts, Nidya, or Kazanji, since Flying units are useful for getting behind enemy lines in combat.

The full list of Minor Faction units (and their base stats) is as follows (picture because COLOURS, ROYG - red being the worst and green being the best):



-Note-
Keep in mind that these are the base values for each unit and they will vary depending on a) equipment you put on unit and for production b) game speed c) technological era.