Lincoln was shot in Ford theatre and Booth was caught in a barn, not a warehouse.
Here's some differences though :
Lincoln was a Republican, Kennedy was a Democrat.
Lincoln was born poor in a filthy loghouse, Kennedy was born filthy rich in a mansion.
Lincoln was tall (6'6"), Kennedy was relatively short (5'10").
Lincoln was a loyal husband, never leaving Mary Todd even when she was mentally unstable, Kennedy was the swinger of the 60s.
Lincoln was a wartime president but never fought in a war, Kennedy fought in WWII but presided over a Cold War period.
Lincoln's son Robert was a Cabinet politician, Kennedy's son John was a closet politician.
Lincoln died in his 50s, Kennedy died in his 40s.
Lincoln was a Christian, Kennedy was a Catholic.
Lincoln wrote his own speeches, Kennedy has most of his written by ghostwriter Ted Sorensen.
Lincoln died one day after he was shot, Kennedy died immediately.
Lincoln was "The Great Emancipator," liberating thousands of slaves from the cotton fields of the south, Kennedy liberated women down south.