If the homes are owned separately, filing separately might allow for each spouse to separately exclude the gain.
However, if the homes are owned jointly, then you would each half to report half of each of the two sales and you can't exclude the sale of two separate main homes, even though each might have met the definition if sold in different years.
You get one exclusion every two years (one home, one sale). When more than one "main home" meets the definition, you must choose the one on which you wish to exclude the capital gain.
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