Another thought occured to me on the 'waging war' system. Everyone knows you can't right without resources (money, troops, etc.). So, let's say your nation/group gives you about 10,000 Gold (I'm planning on a silver based economy, so the Gold would count as a 'special' currency). You then use this to gather your army. Now, you could either flesh this out to grant actual 'red shirt' characters, with your MC's 'elite' characters as Captain/Commanders; or keep the army as a variable that unlocks certain 'missions' (quests) that chain. Example: you've got three towns between you and the next Main Quest. You get mainly spear units, Town A and Town B show up on the map as 'quest available'. Add a couple of sword units and a calvery unit, Town C shows as available.
If I remember right,
Romancing SaGa 3 did that economy part, like, you taxed your subjects and developed your army with the funds. Then in the actual battles you had different units, like foot soldiers and cavalry, and you arranged them in a formation... then it played out somehow semi-automatically, while you could give general orders like whether to retreat or to charge all out... Yeah, it's all fuzzy to me now, I'm afraid, and I mostly remember it was too hard for me.
As for ideas about what this war scenario could be like, I'd totally dig it if it wasn't a bland "conquer your neighbour", but something more like a civil war, where you have your cousin or whatever competing for the throne, and you have to fight your own dudes to beat him.
Also, what I'd like is if the whole war thing was closely tied to the main plot. Like, you'd get to adventure like in any general JRPG, but then you'd have both optional and mandatory battles where you'd have to lead your army, and you could get your general staff to develop the army in the meanwhile, aaannd... stuff. Like, there would be political scheming and plots and escaping from dungeons and stuff, and then there'd be large-scale battles and a big horn orchestra playing in the background.

And, like, if you hated the managerial side of things, you could just delegate more of the responsibility to your trusted advisors and just lead personally from the front... just like a real prince/princess/whatever!
I dunno if that was what you were thinking at all, buuut... yeah.

It's just me, that's the kind of game I'd love to play!