Do you have a preference Fannie vs Freedie ?
Freddie is actually in a better position from a financial perspective as they have paid the Treasury more on a percentage basis than they received as compared to Fannie. If they decide to use the "dividend" payments and count that as payment on principle on the original loan + 10% interest (personally I think it'll be lowered to 5%), then Freddie would be fully repaid or will likely be paid after they report Q4 2016 results and make one final payment.
There is a small possibility that Freddie could start paying Dividends on their Pref shares 1-2 quarters before Fannie, which would cause their Preferreds to hold a higher premium to Fannie's (which is currently the opposite of what the market is pricing in, but markets arent always efficient)
Fannie Mae does have a much larger market share, but keep in mind the Government seems to be pushing towards a Single Security (CSP). This benefits Freddie as it will allow them to steal market share from Fannie. All in all, you can't really go wrong with either. I'm split 55% Fannie and 45% Freddie, but tend to swap when arbitrage presents itself. My focus is always on FNMFN and FMCCT due to their yield and historical premium to Par. I also like FMCCP and FMCKJ. FMCKJ has a 5-year Call restriction (2012, 2017, 2022) which would prevent it from getting Called by the company until Dec 2022 [since it won't get Called this year]. FNMAS also has a 5-year Call restriction which means it can't get called until Dec 2020. FNMAO and FNMAP also have Call restrictions, but it's only for 2 years and I dont know the dates off-hand. These Preferreds help buy you security and lock-in Divis for a few years, as the Companies are likely to Call [buy back at Par Value or buy on the open market] the higher yielding Prefs at some point and these specific ones can't get Called except on the anniversary dates.
Hope this provides some clarification.