How about a ShadowRun style priority system. For each element you must assign a priority so if you get the best skills you can’t also have the best stats.
Skills: As Guard Captain, As Patrol Leader, As Patrol Guard, As Mouse Guard, As Tenderpaw
Rank: Guard Captain, Patrol Leader, Patrol Guard, Mouse Guard, Tenderpaw
Nature: 6, 5, 4, 3, 2
Traits: 4, 3, 3, 2, 2
Stats: (6,2), (5,3), (4,4), (4,3), (4,3)
Skill: Allows you to select your skills, with the questions in the recruitment chapter, as that rank.
Rank: Determines your status, and you answer the Circles and Resources questions as that rank.
Nature: Sets your nature rating but you must now accept all restrictions of the questions in recruitment chapter.
Traits: Choose your hometown to fit one of your traits. Tell us where the others come from.
Stats: Put each number into either Health or Will.
This may result in characters that are totally inappropriate at their role such as the captain with no skill. But you can mess around with it until you think it’s balanced.
Priority 1: Traits - I get a mighty 4 traits. I could elevate them but I’ll keep them all at 1 so I can have more ways to earn checks.
Priority 2: Skills - I answer the questions about skills as a Patrol Leader.
Priority 3: Stats - I get 4 in both Health and Will.
Priority 4: Rank - I am a Mouse Guard with the resources and connections to go with it.
Priority 5: Nature - I’m not a mousy mouse. I will learn skills faster though! What a twink!
Even further you could switch out the priority numbers so instead of priorities 1, 2, 3, 4, 5 you could have 2, 2, 3, 3, 5 as long as they add up to 15.