There's a couple of things I worry about with strongholds.
For me, the whole game could be about building something up. I'm a builder at heart.
My biggest worry is that the Stronghold a player builds will be "upgraded" to a maximum and then lose all relevancy, except for the few quests it may offer, and the way it acts as a gold sink by adding merchants and a storage place, and little else.
I would like to see upgrades with purpose and limited by choice.
Say, for example you are a spellcasting class, you may want to construct a "wizards tower" as an upgrade. instead of having this just be a player home, you could for instance think about spells that you can only do here. (because it is a place of power, perhaps thanks to a quest that makes it so, a ritual consecrating the place needing other spellcasters, I trust in the devs imagination here) Perhaps you can choose what type of tower and super spells you can cast here. be it ressurection or powerful curse lifting and healing, or maybe it allows you to divine truths that help you solve quests. cast plague spells on an entire region... whatever, something big.
the point is that in this example your stronghold is functional throughout the game. different classes would have different benefits and choices facing them.
balancing the power of such things can be done by limiting the benefits to only be obtainable at your stronghold, or making them costly (sacrificing XP for effect?)
this way you can also add another gold-sink to your game, without making player wealth seem arbitrary past a certain point.
Edit: Also, I would enjoy it if a stronghold remained accessible throughout most of the game. That wasn't possible in Baldurs Gate: Shadows of Amn, and I found it quite a pity to lose my thieves guild because I had to leave it for a few weeks.