Investors looking into the 2013 market are likely to see housing policy shift to a focus on bolstering refinancing activity and "a tailored principal forgiveness program," said Sarah Hu, an analyst with the Royal Bank of Scotland.

This shift will greatly impact the prepayment landscape in some cases, with Hu estimating that Ed DeMarco's days at the Federal Housing Finance Agency (FHFA) are likely to be numbered.

She added, "mortgage rates will likely be dependent on the duration of QE3, which in turn will have a profound impact on prepayments."

Hu sees the the housing market in a recovery phase, but not in a boom phase. 

"While rising home values will be a welcome relief to our economy, many borrowers will remain underwater on their mortgages," Hu pointed out. "Nonetheless, involuntary prepayments could decline with an improving housing market. Moreover, rising g-fees and wider primary-secondary spreads will continue to increase borrowing costs, hindering refinance ability."

Hu added that higher coupons will face more potential headwinds from changing housing policies, while loan balance paper is less sensitive to HARP adjustments. To be sure, the Mortgage Bankers Association warned in October it expects to see $1.3 trillion in mortgage originations during 2013. This is down more than 25% from its revised estimation of $1.7 trillion in 2012.

Refinances are expected to fall to $785 billion in 2013, down from a revised estimate of $1.2 trillion in 2012.

"The prepayments of streamlined FHA loans resemble that of VA loans for pre-June 2009 originations. Both will likely prepay fast in 2013. By comparison, 2010 and 2011 GNMA production provides solid prepayment protection due to their higher insurance premium hurdle," Hu explained.