I think if you’re going to rewrite the Craft system you should rewrite the Charm system at the same time to supplement it.
Basically, the point of Craft in a purely gamist1 perspective is to give your characters Cool Stuff that does Neat Things. Those neat things can be simple (“I get a +2 to hit!”) or complex (“When I hit with the sword I get to summon a orbiting fireball that acts as a mobile shield, I can have up to five of them and when I strike I can expend all fireballs to do a super attack!”) or anywhere in between.
Simple effects are remarkably easy to balance; just set a maximum effect bonus (max dice bonus = Craft is a good one) from Cool Stuff, declare bonus from multiple Cool Stuff does not stack, only the highest applies. Then it’s just a matter of setting a cost for this and determining how much downtime is required.
The good thing about this is it is a system you can use to include all sorts of downtime activities for other players as well by adapting it whole. You want to craft a magic sword Artifact 5 (+5 to swording) and that’s cool. Your Eclipse wants to set up a functional administration for that city you took over, the Zenith wants to raise a temple, the Dawn wants to train a militia and the Night wants to build a spy network. Okay. So each of these things can be defined as a piece of Cool Stuff that lets you do a Neat Thing better. In this case, we can define them as a simple dice bonus to relevant actions. The Eclipse gains Influence 5 for a +5 bonus to Run Government actions. The Zenith gains Cult 5 and gets a +5 bonus on Prayer actions. The Dawn gains Command 5 and gains +5 bonus on Engage In War actions and the Night gains Contacts 5 and gains a +5 bonus on Gather Information actions. They all build these things based on their own skills (Bureaucracy, Socialize, War and Larceny respectively). The costs, in both resources and downtime, would be the same as for your Sword of Swording +5. If it takes five seasons and a king’s ransom to make a Sword of Swording +5, it takes five seasons and a king’s ransom to make a Accounting Department of Not Being Corrupt +5. Effects which accelerate timeframes, or required Exotic Plot Triggers (think Exotic Ingredients, but call them Things The Players Have To Do In Game Time) are basically going to be the same across frames.
Now everyone gets to make Cool Stuff that does Neat Things while you craft, so its less a one player game and more each player basically spending downtime on whatever.
Of course, this requires you to have a system where Run Government and Invade Country are valid actions with mechanical heft. Doing that for 3e is left as an exercise for the reader.
Once you get past Simple Neat Things for your Cool Stuff to do, that’s going to get trickier. Here is where a revitalized charm system comes into play. Basically any Neat Thing your Cool Stuff can do that isn’t a simple dice bonus is a Charm. I mean, call it an Evocation or a Special Effect or whatever you want, it’s a Charm. This means that you have to balance the list of potential effects against every charmset. Go read some rants about combination hell and see why this is tricky.
Here is how we handle this: We create a new subset of Charms called Universal Charms. These are deliberately weak effects. In terms of power level you’re aiming at the level of Spirit Charms: that is, a set of generic effects that can be tweaked as needed for story effect. Spirits and Godblooded, the two most common enemy types, would be balanced around these Charms and so they would be designed to mainly create interesting effects that are neat, but not very powerful (you want neat and powerful opponents, go fight Exalts or high tier Spirits like Deathlords and Third Circles who have Panoply Charms… but more on that later). The point of the Universal Charm Set is that you can also build them into artifacts. In effect, each Charm would have a cost, a minimum Ability needs to incorporate it, and a time frame required to ‘build’ it. Then players can spend the required resources/downtime/Exotic Plot Triggers and bam, they have a piece of Cool Stuff that does that Neat Thing; ie it replicates the effect of the Charm.
The best part about this is that it also allows you to use this for any of the players’ downtime agendas. Yes, your Twilight can build a palace that has the Charm Mandate of Heaven built into it such that whoever lives in the palace gets bonuses to rulership actions. Or your Eclipse can create a perfectly detailed set of training programs such that the palace eunuchs count as a Magical Bureaucracy which confers Mandate of Heaven upon the leadership of the kingdom. Or maybe your Zenith creates a series of religious dogma that encourage proper obedience and suddenly you have a Magical Cult that grants Mandate of Heaven to the leader of it.
Then there are Panoply Charms, these are the Charms unique to your Exalt type (or powerful spirits, fair folk, whatever). You would tag certain Charms as Panoply-Ok, and they become things you can built into Cool Stuff to trigger the effects of your Exalt Charms on demand. The trick here is that you need a character of that type to use them. So if you build Speed the Wheels into a organization you need a Solar to be running things, at least ostensibly, to trigger this effect. This, by the way, is how you build the First Age. You make building things with Panoply Charms very much more expensive and costly to maintain, and then you have them only useable if the Solars are still around. Then, well, Solars die and…
While this doesn’t eliminate Combination Hell it does reduce it, now you only have to balance two Charmset evers at a time: the Exalt Panoply and the Universal Charms. You can’t ever combine two Panoply Charms from different types, so you don’t have to balance Solar Charms against access to Lunar Charms.
1: No, this isn’t an invitation to start talking GNS theory or defining terms. “Gamist” means “from the perspective of the game as a game.”