That depends much on the GOP nominee. However, I'm sure FDR would beat all of the modern GOP contenders (even Hillary in a primary).
Best scenario, with Jeb Bush as challenger:
Franklin D. Roosevelt/Hillary Clinton: 347 EV. (53.2%)Jeb Bush/Scott Walker: 191 EV. (46.0%)Worst scenario for the GOP with a Tea-Party Ticket (however, a Cruz-Bachman tickt is very unlikely; but FDR would certainly blow Cruz away):
Franklin D. Roosevelt/Hillary Clinton: 483 EV. (59.0%)Ted Cruz/Michele Bachman: 55 EV. (39.0%)