It depends.
Filing as Married Filing Jointly usually provides the greatest tax benefits of the higher standard deduction and lower tax rates.
Generally, in California you need to file using the same filing status as you use for federal purposes. However there is an exception if your nonresident spouse does not have any California source income. Since this applies to you, you would be able to file as Married Filing Separately for California.
For your spouse, if she lived in Michigan but had no income, she may not even have a filing requirement if she did not earn any income while being a resident of Michigan. Please see the following link for more information.
Michigan filing requirements
If this is the case, you would be able to file using the Married Filing Jointly status for your federal return, your part-year California return, and your part-year Oregon return.
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