The biggest con with 5/3/1 is that it's percentage based, once you start pushing big number the small changes in percentages make for big jumps that can be hard to keep up with.
Also, another con is you need to establish your 1RM on your lifts to set the percentages. If you don't work with low reps already, this can be an issue, as you will likely be estimating the working 1RM values.
These are not big cons, 5/3/1 is an excellent all-purpose strength program. I have used it for almost two years with steady gains. Just recently switched to a westside program to focus on powerlifting. 5/3/1 has it's roots in the westside method of training.