“Although he is a two-time Academy Award-winning filmmaker, it’s been consistently difficult for him to acquire actors of his preference for most of the films he has directed. Casting Tom Cruise in Born on the Fourth of July (1989) is the most significant exception where Stone’s top choice was either available or agreed to partake in an Oliver Stone production.”
Does this mean that Tom Cruise was his first choice or not?
I would take it to mean that Cruise was the first choice. If it has been significantly difficult for him to acquire actors of his preference for films he directs and Cruise is the exception then it makes sense.