How you file on the federal return will affect how you can file on the state tax returns and vice versa.
In your case, I would file Joint on the federal. You would then have to file Joint on Michigan, but apply the credit for tax paid to WI for your spouse's income. Wisconsin- you can file as joint and get a credit for the MI tax you paid. She would not include the WI income earned while a IL resident under the reciprocity agreement. Part Year Illinois Joint- include all income while resident (under reciprocity agreement)
The rules that apply are:
MICHIGAN
If a joint federal return was filed, the Michigan return must be married filing jointly.
If the federal return was Married Filing Separately, the Michigan return can be MFS or MFJ
ILLINOIS
Illinois requires the same filing status used on the federal return-if a MFJ Illinois return is filed, both spouses are treated as residents. This election is irrevocable for the tax year. Credit is allowed for income tax paid to another state.
WISCONSIN
You can choose your filing status for Wisconsin- however, if you file separate on the federal return, community property laws apply.
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