Check the rules for 'considered unmarried' to see if she eligible for HOH filing status. 

Depending on income level, credits available, etc.  filing status MFJ or MFS can make a large difference in tax and credits.  

Even with hostile separations (see movie 'War of the Roses').. the  one thing the warring parties will often agree on is that the IRS should get the least amount of tax money (legally)....   If there's a refund involved, you can always direct it sent to multiple accounts (his, hers or its)