It saves data entry effort, with shared information being transferred between taxpayers (for example, address, dependant's personal information, spouse's net income, joint investment information, etc.). Then the software maximizes credits available for both of you (including education, age, medical, charitable, child care, pension amounts, dependant credits, CCB, GST/HST credit, etc.) and determines if there are unused credits on either return. These are transferred from one of you to the other to achieve the best net benefit to you both.
Also, when you prepare spouse's returns separately, there is a danger of claiming the same credit or expense on both returns. This can result in the CRA adjusting one or both returns and assessing a penalty based on the adjustment.