Personally I’d like to see several options that you’d need to choose from when you are establishing the original stronghold either by conquest or reward or however Obsidian wants to do it. You’d get three options that represent different specialties: Industrial, Commercial, or Military.
These three specialties would rely on different locations to set their tone. Industrial in a mountainous area, Commercial in the plains or a river area, and the military building could be situated along key road ways. Each of these stronghold types would have a series of add-ons you could build or repair to give various boons to either the stronghold production or your party.
Headquarters: Guild Hall (can upgrade to improve security, goods quality)
Primary Building: Foundry (produces high-quality metals used in other structures or trade)
Primary Building: Ore Mine (generates ore used for the foundry)
Secondary Building: Smithy (grants an equipment boon to your party, either a flat bonus or special equipment)
Secondary Building: Metalworks (produces metal-based trade goods to generate wealth)
Wealth Building: Mint (generates money by using precious ores)
Protection Building: Militia Barracks (equipped miners and craftsman)
Populace Housing: Row Houses (spartan living quarters in close proximity to eachother)
Headquarters: Town Hall (improve to increase security, higher tax income)
Primary Building: Town Market (generates wealth, random chance at unique merchants\items)
Primary Building: Textile Mill (utilizes flax (or other crops) to produce trade goods or special gear)
Secondary Building: Library (research, in-game information repository, bonus to casters)
Secondary Building: Dockyard (allows for greater trade range, boosts wealth production)
Wealth Building: Tax Office (collects taxes from the merchants and farmers)
Protection Building: Town Watch (semi-professional guards)
Populace Housing: Farms and Cottages (generates tax income and supplies the mill)
Headquarters: Motte and Bailey (improve to add stockades for security, more troops)
Primary Building: Armory (better equipment for the party and troops)
Primary Building: Archery Range and Fletcher (allows for professional archers in your troops, bonus to ranged equipment for the party)
Secondary Building: Stable and Road Patrol (increased security, faster travel from the stronghold for the party)
Secondary Building: Training Yard (Bonus stamina to party and troops)
Wealth Building: Toll Booth (generates wealth from collected tolls, better secured roads = more travelers = more tolls)
Protection Building: Army Barracks (professional soldiers)
Populace Housing: Fort Quarters
All three would additionally be able to house a religious structure or two depending on the value of the stronghold. Obviously the more built up the town, the more followers that could exist to a faith. All of these buildings could have 1-3 tiers to allow for continued investment. Possible quests could involve stopping bandit raids on your farms, cleaning out parts of the mines of monsters as mentioned above, assaulting a river-based pirate ship, etc.
All the headquarters would be able to facilitate communication with your companions, a seneschal who helps run the community, and associated NPCs that you could recruit to your town. When you don't have companions with you, they'd provide bonuses to various aspects of the town based on their current skills or class.
The stronghold's primary job should be giving your party boons and wealth, without requiring constant contact. It is an element of the game that can be utilized as much or as little as the player wants. It could utilized basic supply and demand to determine income levels, and just have some simulated events that occur while you're adventuring to add and subtract to the value of the stronghold. There should be no best option for how you go about creating the town, and there could be an investment cap into the place so that it is impossible to upgrade all the building types to their maximum level. If you were confident of your ability to fund the town through adventuring, then you could focus mainly on the party boosts and not the economics.