So I just took Lys since I decided the best way to kill everything would be to knock off the smaller free cities, build up and then move into Westeros. Unfortunately now it seems that the only troops I can recruit from the lone village belong to Lys are all in the merc troop tree.
This is kind of a problem for me, since as far as I can tell if I keep conquering more territory I'll eventually be stuck fielding full merc armies. I did try setting my houses culture to Lys to see if that was how troop types were decided, but it didnt actually change anything. I'm not sure if this is a bug, a feature that's intended to be expanded on later with allowing you to design your own troops or what.
What I did was - I've chosen to be ironborn at the start of a game, not knowing It changes your clture to the one you choose at the start of a game.
So I went full-on attack and wiped Iron islands out and now I'm using Morgh's Troop Editor to choose Unit equipment of culture Ironborn to my liking, since they will eventualy (I hope) all renounce their allegiance with House Ironborn/Greyjoy - They are all imprisoned troughout Essos at the moment.
Same happened when I wiped out Wildlings, but what bothers me is that Iron Islands as a Faction didn't cease to exist/were destroyed like Free folks did, after I took all their Towns/Castles..
Are they scripted to never be destroyed maybe...?
Have you tried increasing your rep with the villages after you made the culture change. so like when you first take a town the villages still have the old type recruits and it takes time or an increase of rep with the village to accelerate the troop type change to your culture