During our separation (two tax years) I created two sets of tax returns each year -- one filing jointly, the other two forms as married but filing separate. I then presented them to now ex to allow her to decide which she wanted to go with -- either commingling the incomes and deductions together and splitting 50-50, or else separating all these separately along purely personal lines. She always chose the joint return because my income and my deductions were much more substantial at the time compared to her own -- she came out far better ahead than on her own.
Perhaps you might be able to figure it out a couple of different ways and choose the one that offers the best solution for either or both of you? Not sure if it would be worth the effort in your case or not, but just a thought.
