Power of Rule: As presidents, FDR and Lincoln have some rather stark similarities. Lincoln wielded way more power than most presidents due to the simple fact that he no longer had to govern his enemies, and was now free to enlist cannons to make his points. Nonetheless, he used his power to restore the Union and the legacy of a single national identity can be seen as irrefutable proof of Lincoln's abilities as a leader.
Likewise, in the wake of Roosevelt's election during our greatest financial crisis, Congress pretty much abdicated and did whatever FDR wanted, and with Democratic congresses throughout his term, he was very successful in getting his way. Only the Supreme Court stood up to him, causing Roosevelt to try a laughable scheme to appoint more than nine justices in order to sway the court his way. Straight from the frying pan and into the fire, the country trusted him with more power and a longer reign than any other chief executive, and his work continues today.
Rule of Rower: Let's talk kicking ass. Lincoln is clearly an army of one, Josey Wales in better hat and more kung fu. His battle is personal, and like Batman he has turned himself into a living weapon driven by emotion. The axe is an awesome weapon, giving him a sharp edge, crushing weight, range from the length, leverage from a low grip, the ability to utilize the handle as a shield, and powerful if albeit single-use range attack. In a strict one-on-one fight, Lincoln is the clear winner.
Which is why FDR is so deadly an opponent. He is more methodical and cautious than Lincoln due to his condition. To continue the comic-book analogy, FDR is Lex Luthor, driven, brilliant and most of all armed to the teeth clenching his cigarette. He knows that Lincoln can take him in a fair fight, so to quote Captain Jack Sparrow, "That doesn't give me much incentive to fight fair." Between these two presidents are the acmes of two archetypes, might vs. mind, heart vs. skill, nature vs. technology, Gryffindor vs. Slytherin. In this case, they are oddly even.
Let's Talk About Sex: In this, there can be no contest. FDR has Eleanor, played by Lin Shaye... not exactly someone you'd paint on the side of a bomber. By contrast, Mary Elizabeth Winstead was cast for Mary Todd Lincoln, and scientists use her to calibrate instruments that measure the temperature of stars, she's so freakin' hot. Plus, Mary Todd was into occultism, dressed in black and talked to the dead, so she's also rocking the hot goth girl thing.
Arch Nemesises... Nemesi: Point to FDR in this regard, as werewolves are almost always more badass than vampires. Van Helsing, Twilight, Monster Squad, you name it, and most times vampires go up against werewolves it's the furries who triumph. Plus, they're Nazis, and everyone knows that Nazis always get final boss status.
Final Verdict: In the end we believe that FDR's superior firepower, tempering against a greater opponent, and his analytical nature will be the deciding factor in making him the winner. That being said, Lincoln may not carry the day, but he will look a million times more awesome and score a lot more tail while doing it. Expect him to go out in a blaze of glory, a martyr, hero and inspiration to those who will continue the fight in his honor... which, make no bones about, it is exactly how the last Batman film will end.