Base building is a pretty cool feature in many games, but I don’t think it would fit well into this one.
As I see it you’ll be moving from town to town, trying to make the most out of your ressources. Is the player going to spent his time and money on travelling back and forth to his base? How much would he use it?
And what would the base be for? What would it function be? Training? Resting?
I can’t really see another way to train than fighting and it’s fine the way it is now (with the skills redone).
Resting, well maybe battle brothers can heal faster when staying in a town.
Or…
Instead of a base you can order your brothers to set up a camp. This will cost you some tools, but your mercenaries recover faster and if you’re attacked, you’ll start in a strong defensive position. If you’ve been camping for a long time your camp will even be fortified with palisades or wooden stakes.