What I like about 5/3/1:
I like 5/3/1 for many reasons; It's simple, it's abbreviated, it focuses on major compound lifts, it's adjustable, it's progressive, and it has enough volume at higher percentages.
My biggest issue with 5/3/1:
When you start 5/3/1 you are NOT handling really heavy weight but you are getting in some good reps. As you progress you are handling heavier weights but you are not getting a lot of rep work. For beginners and intermediate lifters, I think the progression to the heavier weights is fantastic but I also think that reps are needed to continue to get bigger and drive more strength gains.
To be fair, Wendler seems to address this issue in his "Beyond" book and has made some good adjustments.