Different things work for different people. Templates are good for beginners, but once you realize something isn't working for you, you need to do something differently. In my opinion, it is all about knowing your body and how you respond to certain things. Once you start to figure that out, adjust accordingly. It is all a learning process, and a marathon...not a sprint.
Personally, I tried 5/3/1 for about 8 weeks and just didn't like it. I don't doubt that it is a great program, I just found it lacking a certain level of intensity. I'm sure I would make gains on the program if I stuck with it, but if I am not enjoying training then what's the point?