Oh, they were very clear on the predestination paradox -- the characters in season 1 don't know the rules yet, but the writers do. Admittedly, season 1 is the weakest of the 4 seasons and IMO season 2 is where it becomes the show it wants to be but it needed season 1 to build the foundations and rules of time travel. Things hit their stride especially when Jennifer gets more involved with Team Splinter and let me tell you, I didn't expect to love Deacon in fact, I was against it. But by the end of the show Jennifer and Deacon become my favorite* (I like Shaw but Shaw has nothing on Deacon).
But 12 Monkeys knows its rules, on a recent rewatch as I was watching an episode of the last season, I decided to watch an episode in season 1 and I was hit with a lightning bolt when I realized that the thing in season 4 was set up and comes back around to season 1.
*(Honestly though my main favorite in terms of complexity messiness, and sheer bloody-mindedness is a tie between Jones and Cassie -- who undergoes a huge change in arc. It's amazing.)
Aside from the writing, I also have to credit the music and the editing, without the editing for 12 Monkeys, it would be more difficult to understand but the editing wins in a way that no matter what time they end up with I know what's happening. Also, this show's foreshadowing, callbacks, and call forwards are just great. Sorry for raving about the show in this thread but I just wish more people knew about this show.