As for the "why", I couldn't begin to speculate but the Married Filing Separately (MFS) status is punitive in many ways and does not allow a number of credits or deductions that are allowed with other filing statuses.
You can carry the losses forward, and you do have the option to amend your wife's tax return to add your income and file jointly. While it's difficult (or impossible after certain deadlines) to amend a joint return to separate, you can easily amend the other way around and you may find it beneficial.
My advice - file an extension now (and make a payment if you expect you may owe taxes, to reduce or eliminate any potential penalties or interest.) (File an extension here: TurboTax Easy Extension)
Then take a look at what a jointly filed return will look like (if your wife agrees, she must be amenable to filing jointly if you make this change.)
You can always abandon an amendment if the result doesn't turn out better for the both of you.
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