MFS you lose the deduction for student loan interest, the earned income credit, education tax credits, credit for child and dependent care expenses, retirement contributions may be limited, dependent tax credit may be reduced.
an extreme example would be if you had 3 kids and qualified for the maximum earned income credit which would be over $7400. that with other lost deductions and credits could well exceed the extra money you would have to pay on the loan. Also, when you're old enough to start drawing social security 85% (the maximum amount taxable) is automatically taxed even if your combined incomes would result in a lower % being taxed.
you both must use either the standard deduction or itemized deductions.
there is no way for us to know whether MFS is better than joint in your situation. you would need to prepare 3 returns. one MFS for each of you and one Joint. Not really feasible with online, but you can do as many rturns as you want with any of the desktop versions for a single fee.
