FC3 was the best for me, because Jason Brody was a character himself and you could track his growth (and/or devolution), alongside his relationships with his NPC allies. The Far Cry games where you can make your own character have to be dropping you in as a blank avatar, and so they lose out on that characterization.
And that was crucial, to me at least. Vaas wasn't just an entertainingly crazy antagonist; he was a legitimate foil for the PC because you were also going violently crazy. Conversely, in FC4, Pagan Min had a relationship with you, and it was well-done, but Ajay was so bland himself and did so little growth as a character that there was nothing to carry the arc.
I have low expectations for this game, because if you can't make the protagonist a character because you need them to be an empty customizable vessel, you can't tell their story.