I wuv me 5/3/1. well actually I do a mix of the 2 and westside, so yeah.. but I use the 5/3/1 progression method and "template"
IME it depends how good you are with your big lifts. If youre having technique / form problems dont do 5/3/1 because you arent doing many sets of it. 5x5 would be better to start off with if youre more on the novice side.
pros Id say 5x5 youre gonna gain a lot faster but stall quicker
cons 5/3/1 is slow progression but you can add more, than again you will just stall faster. I finally have stalled on some lifts on 5/3/1.