It depends. In reality, these two states take the same situation, and treat them virtually the same way, but it doesn't seem so when you read the state explanation of each. But, here is how you file:
Kansas. As you state, Kansas requires you to file a joint return, using the nonresident status (even though your wife is a resident). They do this so that only your wife's income is actually taxed in Kansas. Your income is excluded in Kansas. A nonresident of Kansas does not pay income tax in Kansas if their income was not earned there. By treating her as a nonresident, her income earned in Kansas is taxed, but yours is not.
Michigan. Michigan also requires you to file as Married Filing Joint. However, Michigan requires you to file a resident return, although they also require that the nonresident form be filled out (TurboTax will do this automatically) for the spouse that does not live in Michigan. While that income is factored in to determine the total Michigan tax, a credit is given against this nonresident income so that it is not taxed in Michigan.
Yes, that can sound a bit confusing, but the end result is the same: Kansas in essence only taxes your wife's income, and Michigan only taxes your income. Neither need you to file the form or schedule to have credits for taxes paid to other states because neither is taxing the other state's income.
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