In RTR after the capture of the province U need to carry out cultural assimilation (there are... 3 levels?), which allows larger number of available units at the next levels of the barracks; at the lowest level of the barracks, you can recruit units of the lowest regional level and at the highest level barracks U can recruit elite units characteristic for Ur nation. After succesful conquer of province you first need to pacify it, and then choose the type of control that you will be held on it. In EB are 3 types of control: full incorporation, subordination, the status of ally, and a puppet state which allows the recruitment of General/Governor. The higher the degree of subordination the higher level of the barracks you can build a national and thus more types of its units you can recruit. The lower degree of subordination the higher level of regional barracks U can build and more types of such units U can muster.
Another thing is that some factional units U can recruit only in some provinces and same thing with factional units; use RECRUITMENT VIEWER for help with this.