Bruce Martin argues for why the Kennedy-Lincoln parallels are probably just coincidences.
Bruce Martin, "Coincidences: Remarkable or Random?" Skeptical Inquirer (September/October 1998): 23–28
Abraham Lincoln and John Kennedy
It is always possible to comb random data to find some regularities. A well-known qualitative example is the comparison of coincidences in the lives of Abraham Lincoln and John Kennedy, two presidents with seven letters in their last names, and elected to office 100 years apart, 1860 and 1960. Both were assassinated on Friday in the presence of their wives, Lincoln in Ford's theater and Kennedy in an automobile made by the Ford motor company. Both assassins went by three names: John Wilkes Booth and Lee Harvey Oswald, with fifteen letters in each complete name. Oswald shot Kennedy from a warehouse and fled to a theater, and Boom shot Lincoln in a theater and fled to a barn (a kind of warehouse). Both succeeding vice-presidents were southern Democrats and former senators named Johnson (Andrew and Lyndon), with thirteen letters in their names and born 100 years apart, 1808 and 1908.
But if we compare other relevant attributes we fail to find coincidences. Lincoln and Kennedy were born and died in different months, dates, and states, and neither date is 100 years apart. Their ages at death were different, as were the names of their wives. Of course, had any of these features corresponded for the two presidents, it would have been included in the list of "mysterious" coincidences. For any two people with reasonably eventful lives it is possible to find coincidences between them. Two people meeting at a party often find some striking coincidence between them, but what it is—birthdate, hometown, etc.—is not predicted in advance.