So what I need help with is:
Nature? Should I do just one for all exalts, or one for each type?
Obstacles: Exalts (Mice), Mortals (Animals), ? (Weather), ? (Wilderness)
Can anyone think of a way to do charms? Maybe I could do excellencies by allowing different shades of dice (as per BW)
Also a skill list! I could just port over from Exalted, but not all of them are probably needed.
Focus on one type of Exalt.
I would go with Dragon Blooded, myself… but whatever interests you is cool.
Nature is as much an obstacle as it is a benefit, as I understand it now. Stick to one type for your chosen Exalts. Solars or Dragon Blooded might be the easiest to go with, or use Solars versus Abyssal-Weasels. Don’t try to do everything at once or else your Hack writing is going to blow up & get too complicated. Pick your protagonist Exalts and your antagonists.
Charms? For Jedi abilities, I was thinking of just using weapons/tools… but it wouldn’t work for combat stuff. It’s a complicated thing to bolt on top of your skills & weapons. Traits, maybe?
The Exalted list isn’t quite as extensive as Mouse Guard, and the focus is far different than the skill list for Mouse Guard. That’ll be a bitch to wrangle, but you’ll have to feel it out.
First, you have to decide on what mechanical/color level you want your hack to operate on. I don’t really have a way to articulate that succinctly, but what I’m getting at is…in Mouse Guard, the players are only going to play guardmice. They won’t be playing craftmice, scientists, mayors, day-laborers, whatever. Just guardmice. So the rules don’t actually have to cover those other types of mice, except as their paths cross with guardmice, and even then only from the perspective of guardmice. You could swap “guardmice” with “Dragon-Blooded” or “Solars” or what have you, and have an Exalted hack. Then, rewards points become Charms, tapping Nature becomes wielding overpowering Essence, swords become daiklaves, halberds become grand daiklaves or whatever…very little actual mechanical change is needed, you’re just re-coloring everything. At that point, I think all you need to worry about is Nature, and perhaps a bit of skill tweaking here and there.
If you’re interested in more mechanical tinkering, then we have a whole other kettle of fish to deal with. Before I go off the deep end with mad science hacks, I think I should wait to see where you want your hack to be. 
-B
I’m stuck in LAX for another hour (verily it is the 459th layer of H*ll. I escaped the 391st layer earlier today, IAD/Washington Dulles)… So, random thoughts/mad scientist here. Use them or not, doesn’t matter.
Recruitment… Ditch the Tenderpaw, Guardmouse, Patrol Leader concepts. Maybe use Castes instead. You’ll have to rebalance the skill point distribution later, though. However, Dawn caste Solars should have different Health/Will than Night caste, etc.
Charms… Maybe specific chains of moves in Conflicts trigger a charm effect. Attack-Maneuver-Defend is the “Sparkly Vampiric Prana” in Fight conflicts, or Defend-Feint-Maneuver is the “Happy Happy Joy Joy Technique” in the oratory thing. It’ll add another layer of complication onto the system, though.
Fucking United… Edit: I think those assholes stole our plane to use for another flight. Maybe I should try to get to San Francisco instead & stay at my brother’s place. This sucks…