Google search for the phrase "Abraham Lincoln" reveals: 68,200,000 results.
Google search for the phrase "President Lincoln" reveals:   2,430,000 results.
Google search for the phrase "Abe Lincoln" reveals:          3,860,000 results.

Seems the more deferential form of address 'President Lincoln' is the least popular form of reference by a long straw, including the very informal 'Abe Lincoln'. I'd imagine that people's particular fondness for Abe as a significant figure of US history would account for the greater popularity of the familiar term of reference over the deferential. Otherwise I can't imagine the trend for referring to ex-presidents as 'President' catching on so much with dead presidents as with those ex-presidents who are still living.