Both of these movies deal with time travel, I know that is a turn off for some people. Also in both of these movies it’s not that evil overtly wins, it’s more that protagonists fail to prevent the inciting incident from happening. With Paradox it’s not really implied until the last scene what has actually been going on.
I've always felt the protagonists win in 12 Monkeys. They say in the beginning that the virus outbreak can't be prevented (it's not that kind of time travel), but they needed a pure sample of the virus for the future to cure it. I don't want to spoil anything more than I have, but the plane passenger at the end is relevant. They work in insurance.
This is entirely from memory from a time before every Easter egg and explanation was published on the internet, and I haven't watched it in a few years. So I could be wrong.
But I always thought >!the woman on the plane next to the red-haired man with the pre-released, pure virus about to travel around the world, is one of the doctors from the future that was sending Bruce Willis back to locate a pure sample of the virus so they could develop a cure in the future. As she introduces herself, she says she works "in insurance." So I always took that to mean their original goal was successful. !<
Regardless I need to watch this movie again. It is easily one of my favorites and the first movie that made me realize just how amazing an actor Brad Pitt is and that he wasn't just another pretty face in Hollywood.