You can still use percentage training in something like WS4SB, Wendler didn't pioneer percentage training, he just make it simple for your average person. On another 5/3/1 note I have heard of Jim recommending doing power cleans or power snatches before your deadlift or squat work, so you can give that a shot if you are really craving some speed/explosive training.
Personally, I think traditional DE work (speed bench/squat) is overrated, with the exception of speed pulls. If I am going to do some sort of speed work I prefer plyometrics or olympic lifts.
I would recommend either 5/3/1 with power cleans/snatches, or doing WS4SB and paying attention to percentages you are training at. With WS4SB, just work hard but don't over do it, then test your max every month or so.