IV. So it would just be a mesh between Sim City and Warcraft/Starcraft? I'm fine with that. In fact, aside from that, I do think your idea's certainly making good use of the time-gating mechanic. The part about having quests only open up after a certain level of upgrading, I mean. Perhaps your stronghold could be a temporary home for refugees of some village while you go clear the area and make the land safe? Stuff like that would be neat.
V. I dislike the idea of having a skill that summons a band of NPCs to fight with you, even more if they are generics. If you had the opportunity to create that personal squad of bodyguards with the Hall, though, that idea doesn't sound quite so bad. Also, I don't really like the idea of having them pop out of nowhere. Maybe the research into a portal stones could be a stronghold option that then unlocks the skill to call upon them? Other than those two issues, I like the idea.
VI. I actually like the idea of training villagers and party members. If in addition to that and after returning from training that party member could act as your personal crafter that you can request jobs from, that would be super. Expanding on the idea of researching portal stones in V, jobs like researching those kinds of magical devices or weapons that can cleave the earth could act as EXP troves for the lower-leveled characters. Furthermore, that would actually give reason to make a character or use an existing npc for the sole purpose of crafting and would give added permanent gameplay bonuses to investing in leveling up a different character.
For V, I meant for the stronghold's army / security force to be a completely separate mechanic from the personal security.
The stornghold forces would be upgraded in mass. Say you have archers, infantry and cavalry. You could equip each one through a simple, generic interface. Maybe like a tiered progression. For example, infantry start out with normal weapons and armour - say chainmail and a longsword. You could upgrade to +1, then +2, however bonuses work. And perhaps even take them from chainmail to splint mail, plate mail, full plate, etc. The only change you would see is maybe their color, and you would have a card that you could view which showed each type of troop's stats. As far as actual fighting goes, it would be like a RTS where the outcome is calculated and you see the results after. Bigger bonuses insure less casualties, and allow you to have more battles without much recovery time to rebuild the army. I pictured it being a fairly simplistic system so it doesn't require an impossible amount of resources to include in a game. It is essentially a meta game gold sink after all.
The personal security force I envisioned being more customizable. Like a small group of npcs you could give left over items to, and which would use them in battle as the AI permits. How they get into and out of battle could be upgradable I suppose, where initially you have restricted access to them and later gain the ability for them to join instantly.
I don't know specifics on either of these, either mechanic could work in a total different manner, all that matters is they function as a gold sink. I'm sure Obsidian will cook up something that satisfies, and I would wager it will be drastically different than anything I suggested. I'm looking forward to seeing what they came up with!