WASHINGTON, Jan 14 (Reuters) - The Treasury Department announced on Thursday it was overhauling its stake in Fannie Mae and Freddie Mac, charting a course for the housing giants to slowly rebuild their capital with an eye towards eventually letting them issue public stock and escape government control. The changes would allow the pair to retain profits in exchange for giving the Treasury a larger stake, but envisions years of rebuilding capital cushions before they could pay out dividends to investors or exit government control. Government officials also acknowledged that a number of complicated issues must still be resolved by the incoming Biden administration. (Reporting by Pete Schroeder Editing by Chris Reese)