Have you read "Beyond 5/3/1" yet? It has a TON of new variations of BBB along with the introduction of FSL and Joker sets etc. Many of those variations of BBB have you going up to your first set percentage AND BEYOND.
The original poster asked about advantages/disadvantages to running either FSL/BBB. One issue with that question is that "Beyond 5/3/1" just came out back in July so there has only been like 6 months of experimentation done with the FSL and other new programming.
I can tell you from personal experience that when "Beyond 5/3/1" came out I had been running BBB and slight variations of BBB since starting 5/3/1 back in February 2012. In the spring of 2012 I was stalling out, regressing and getting stuck on the chest/shoulders/hole/floor of my lifts (RAW lifter). I switched my assistance to the FSL paused reps (5x5 set/rep scheme) and saw immediate improvements and spent July-October PRing on almost every lift during each workout.
The beginning of October I hit a wall again. My work schedule changed to working an overnight shift Wed-Sat so I'm never getting enough sleep which in turn causes me to really lose my appetite and I'm also taking sedatives to get what little sleep I can. I can't just quit my job so I've had to man up and find other ways to keep getting stronger.
First off I dropped my TM and I've also switched back to the BBB for a few cycles. I believe that switching to the FSL paused reps really helped me to breakthrough some sticking points for those couple of months BUT the fact that I was never going above 5 reps during my assistance work was causing me to lose some endurance strength.
I haven't beat my PRs that I set the final week in September BUT now my lifts are trending back upwards and I can see that if I gut it out for a couple of more cycles I'll beat those PRs. This is even more encouraging when I consider the fact that I was 240lbs the final week of Sep and now I'm down to 225lbs.
So what's the point of this rant? The point is that there are positives and negatives of FSL and BBB but what you've got to figure out are your goals, your current capabilities and what is going to help you over the next few training cycles. Jim lays out some like a 6-12 month training plan in "Beyond 5/3/1" but there isn't any reason why an intermediate lifter can't do the same based on the plethora of options presented in "Beyond 5/3/1"
I've kinda got my year of training planned out. I don't have hard dates set for when to switch assistance work but I can see the flow:
Presently I'm running BBB and just about every other week I switch the 5x10 to an alternate exercise. I have multiple bars so I'm able to do SS Bar squats (free and box), trap bar deadlift, swiss bar bench press, swiss bar overhead press and also I can try multiple grip widths on bench and overhead with the straight bar or swiss bar. I generally do Joker sets on 3x3 week and Joker singles on 5/3/1 weeks. I plan on doing BBB for 3 of the 7 week cycles.
Next I will flow into FSL 5x8 sets/reps. I'll still switch out the bars some but not nearly as much as during BBB. This is will be done for 1-2 of the 7 week cycles.
Then I will probably go with FSL paused reps (5x5). There will be no swapping out bars during this phase. In the book Jim recommends this for the squat, bench and press but didn't mention anything about the deadlift with this assistance. During this phase I COMPLETELY reset after each rep of deadlifts during the assistance. The main sets I will touch and go (no bounce) but my assistance reps are completely paused and completely reset in the case of the DL. This will be done for 1 (maybe 2) of the 7 week cycles.
Next I will either do 5/3/1 and dynamic work assistance for 1 cycle or go back to the BBB as described above.
That is what my training year is going to look like.
Clarification: Although I swap out barbells and boxes and stuff for my assistance lifts I don't change up my main lifts except in the case of injury. I do straight bar squats, benches, presses and deadlifts. I have done box squats for a few cycles due to a back injury but I would rather do free squats.