I will always go with the classic 1989. Not only because of nostalgia, but because of several reasons.
First, as some of you pointed out, it make no sense....the minifigure head is flat only to attach the rest of the head to complete it (that being hair or a hat and so on). Also, like many of you, I had to read about it first in order to understand the logic behind the flat skull head.
Makes a great point about it:
Second, and this is going to be controversial, I don't like the design of the pirates of the second and third wave. Probably because I'm extremely conservative, but in my opinion they made them too cartoony and campy. It's like they took the first series and made them more child friendly (which I'm sure they did...being a product intended for kids), but for me it was far too different than the original.