We don't have militia in BC, instead we have levies. They are the same thing of course.
In BC cities allow the recruitment of levies (militia) and castles allow the recruitment of semi-professional and professional warriors. Levies have slow replenishment rates, and smaller pools. Cities also have less recruitment slots (number of units that can be recruited in one turn). Levies are recruited according to the region the city is in, and not the faction. When the player is in Iran he can recruit Iranian levies, when he is in Anatolia, he may recruit Anatolian levies and so on.
Some factions get fairly well tech'd up castles at the start of the campaign, others don't. Starting 'stacks' are normally 30 to 100% full, and usually consist of a range of units from poor to elite. The AI is coded to recruit units in accordance to how we feel that faction historically fought. AI armies will generally consist of no more than about 10 - 20% levies, the rest will be semi professional and professional units.
Some factions are surrounded by rebel settlements. For example the rajputs, kypchaks and khwarezm have a healthy ring of rebel settlements to subdue. However most factions are already bordering their enemies. For example The Kingdom of Jerusalem, turks and Armenia have very little room to manouver and very few rebel settlements around them to grab.
Rebel settlements are a fact of having a large scale mod, and I feel they are a part of the overall strategic gameplay.
Each faction in BC has a unique set of atleast 13 semi professional/professional units, the average is probably closer to 15. There is no "cloning and re-colouring" of units, however some units are recruited among 2 factions. For example both the Ayyubids and Omani's can recruit Magrehbi marines, both Khwarezm and Seljuks can recruit western turkomans etc. These are units we know were used by both therefore we allow them both to recruit them. In many cases sub-regional units were made, for example I made 3 different regions of turkic units.
In vanilla M2TW many factions were clones of each other, for example Portugal and Spain were practically the same, Milan, Venice and papal states were practically the same. In BC, we really have nothing like this, every faction feels unique and fights in a distinctive style.
I hope I have answered your questions, and thanks for your interest.
Cheers