I think integrating the stronghold with the world at large might be too much work, but there is a possible compromise here.
IMO, PoE can be viewed as two separate games - the Icewind Dale-esque romp of Caed Nua + The Endless Paths, with the Adra Dragon as the final boss, and, well, everything else. When you go to and from your stronghold, it feels like you're switching between two games. This is actually cool, it gives the world a feeling of breadth.
So what they could have done is found a way to integrate the stronghold mechanics with what's going on in the dungeon. Like, I dunno, off the top of my head, establishing relationships with the "Underdark" factions like the Vithrak, hiring people to excavate new rooms or haul off the dragon's horde, stuff like that. You could put in all sorts of little bits of choice and consequence in there.