I have the BMS and am very happy with it. I installed it a week after I got my car, owners manual break-in is overrated just use the mototune break-in procedure for a strong long lasting motor!
Burger Tuning has been around for a while and has a lot of experience tuning BMW's. aFe on the other hand seems like they are new to BMW tuning.
Also with the BMS if they come out with updates you can update your unit via USB, aFe doesn't offer this.