Legally you both are free to file either married filing jointly or married filing separately, therefore, either way that should not present any issues for your naturalization case.
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Not if even though each of you files separately (to avoid the "marriage tax penalty" ? ) you each declare to be "married" on your tax returns.
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Not if the marriage was bona fide and no fraud involved. How you file your taxes is between you, your wife, your respective consciences and the CPA who prepares the taxes.
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