Have you considered roving 'windstorms' on the strategic map that you could be caught in in the same manner as when the counter ran out in the old system? They could be unpredictable and harder to avoid both at higher difficulties and when far from a shelter.
I thought about that quite a bit, actually, but it's a bit Zelda 2. Which I like, but others probably wouldn't as much. And at the moment, it's not possible to do realtime game simulation on the world map in the sense of dodging things and getting hit by things. It's well, a map, at the moment. The challenge is making all that stuff synchronous in multiplayer, which is something we always consider; so that would be a really, really major extension to the underpinnings of the game at the moment.
I think roving windstorms sounds like an awesome idea. Per the "Which I like, but others probably wouldn't as much.", that sounds like it would be a feature that fits the "Options" menu well - if difficulty can be changed on the fly, windstorm frequency could hypothetically be done too, couldn't it?
Of course, we don't understand the low-level framework you've built the game on, but it seems from the superficial high-level view that the windstorms could function in much the same way that the roaming bandits or ghosts do - if you're making those work on the strategic map in multiplayer, storms could follow a same mechanic?
That would also open up a new NPC class - something like a "meteorologist" - that could show you predictions of where the storms would move on the map?