#1 seems too complicated to me, especially for late-game with large map (as many others have said). And I agree with those who don't love sliders. It's much worse if you have to separately make swords at a blacksmith, as described in the OP, than it would be if they decreed that making a swordsman requires, recruits, iron & blacksmith, so the swords are made automagically when the unit is recruited.
BTW, in any system I think recruits could be sent from town to town like other resources, so you can make large units at small towns if you need to, or ship draftees to the city that has the blacksmith, barracks, and magic-whatever.
I think I could live with #2, #3, etc. No really strong preference, just a few comments....
Most of us are familiar with GalCiv2 asteroid belts. Their resources default to going to the nearest star, but you can redirect them. That could be a good starting point for resources in Elemental. Asteroids come in clusters of about 3, close enough so one player usually has the whole bunch, but if they translate this to Elemental you could direct the ouput of each one to diff cities to even-out resource shortages This would be much more important than in GC2, and much neater than the scheme someone proposed many pages ago to send percentages of the resource to diff cities.
If they did something like that I think they could set up a system which doesn't require too much micro-management, or depend heavily on a hard-to-code AI re-routing things automagically. (If the AI has to decide too much, I worry about how long it takes to code right, and how slow it will run on machines that don't have zillions of fast cores -- AI turns on very large maps HAVE TO run faster than in HOMM5).
1: Give a warning if a city doesn't have the resources to make what you told it to.
2: Have a warehouse building type to store some surplus.
3: Give a warning if a city is about to throw resources away because the warehouse is too full.
4: Have a city screen show how much of each resource the city has and how much it gets every turn (or maybe a summary screen for the whole empire, with one line per city).
5: Remind people in the manual & tutorial that they should check said screen occasionally and redirect resources to the towns that need it.
6: Permit us to send emergency supplies to another city if we need to, perhaps by the kind of caravans that have been discussed a lot above. But if we have been paying attention, this won't happen often.
7: Permit trade between kingdoms. Once the deal is agreed, the transport mechanism works like transfers within the kingdom (same thing if they do vassals & tribute the way I hope).
I think much of this is going to be in the game anyway, and the rest should be easy to write. The point is that they don't have to kill themselves trying too hard.
(Please put the warnings off to the side where we don't have to click on them at once when they appear, and let us read them without making them disappear, in case we want to come back later).
(No strong feelings about whether caravans appear on the map, are subject to attack, how fast they move, etc).
Plan B: I could also be happy if they just had resources like iron mines owned by a single nearby city, and told us to build cities close to the critical resources. Cities would have large & non-overlapping zones of control, larger for big cities. Building a new city reduces the zones of nearby cities. No caravans or transfers between cities. Troops with lousy equipment could be made anywhere you have the barracks (or whatever), but armor could be made only in cities that had iron mines within their zones, magic swords could only be made in cities with some other resource (remember adamantium in MOM?). Don't count units of iron -- if a city has a mine, it has "enough" for whatever troops it recruits. Other things, like gold, might be global. This is almost the MOM approach, except that there would be more kinds of resources, and they might be more common, so there would be some chance of finding a highly strategic location where your new city would have almost everything. Such locations would be worth fighting over -- those might be the decisive battles of the campaign.