I think the arguments against class-based strongholds as well as strongholds themselves are very good. That's why I emphasize again that I prefer a faction system. Which you can join and which have not only one headquarters (stronghold), but several outposts or side(quests) at different times in different places in the game world.
In BG 2 The Shadow Thieves and Cowled Wizards were both found in Athkatla and Trademeet. (It is already known that the Zhentarim are in Waukeen's Rest as well as in Baldur's Gate). Something like that can be expanded. We ourselves don't necessarily have to be boss of a faction / stronghold, as we are wandering adventurers. For me, it would create more immersion to not just complete a specific larger questline of a faction, but to have several small encounters that remind me of my membership in this particular faction in the game world.
Sometimes it's the small details that leave a lasting impression. For example, in DA 2 I really liked that Hawke had to choose between the smugglers and the mercenaries. Unfortunately for me that was too short a membership and in the end just like any other quest line. And yes I also know that in this particular example a "temporary" cooperation was intended, but still found it a pity.
