When your wife didn't file, the IRS created a substitute tax return for her in their computer system based on whatever records they have. But it won't be accurate since it won't have most deductions and credits she might be eligible for. If that substitute return says she owes, they'll hold back any 2016 refund. If it says she is due a refund, they won't pay it until she files.
Your wife should file her 2015 MFS return as soon as she can. If she is due a refund for 2015, you can file 2016 right away, either MFJ or MFS. If she owed for 2015, then you could file MFS now but she should wait at least 6 weeks if she can before she files 2016. If you want to file MFJ for 2016 and she owes for 2015, I would wait at least 6 weeks after filing the 2015 MFS return.
MFS almost always results in higher taxes or lower refunds than MFJ.
