A skewed mix of income and deductions could make separate returns better. If your separate incomes are not close and the lower earning spouse has, say, high medical expenses, it's possible that filing separately may be better. You may be solidly in the top bracket of 39.6 percent and your spouse is in the 15 percent bracket, but the two of you together are still in the top bracket. Or, one spouse may have some business loss deductions from before the marriage that are better kept separate. The cases are relatively rare, and the only way to find out for sure is to do your return both ways and see.
Separate returns can insulate one spouse from trouble.
Maybe you don't know. If you file separately at least you know about yourself. Couples with marriages on the rocks often file separately. But this strategy is not limited to dishonesty. If you are a risk taker, you simply might want to protect your honey.