The $250,000 exclusion will apply to each personal residence that was sold. There is no benefit for filing Married Filing Separately for this situation.
Since you lived in your personal residence for more than 2 years in the 5 year period on the date of the sale, you are eligible for the exclusion.
Since your spouse lived in their home for more than 2 years in the 5 year period on the date of the sale they will be eligible for the $250,000 exclusion on the sale of their home.
