I'm a BSAC diver, and find that for me as a British diver it's the best option. The majority of PADI training is through dive schools and shops, and that doesn't have the social aspect, to me it seems like you spend a few days being taught, then you have to sort out the rest on your own. In a BSAC club there's never a shortage of buddies, and you can take as long as you need to cover the course, without the pressure of thinking "it's costing me more to learn because I'm taking longer".
The major problem with the BSAC system however, is that as a student you are completely dependent upon volunteers for instruction. The instructors aren't paid to teach you to dive, and it can be problematic at times to get training sessions sorted when an instructor is available and willing to instruct. Sadly many of the BSAC instructors I know seem to have taken the instructor route to say "look at me, I'm an instructor" but aren't really as willing to instruct as they could be. One example is a month or so ago I said to one of our instructors that I needed to get my sports diver out of the way asap, but I was told that it would be unlikely to be soon because it depended on what everyone else was doing leisure dive-wise. It wasnt until I informed him that I needed the qualification soon due to my intentions to join the navy as a clearance diver that I got the response that I should have recieved in the first place. Granted, not all instructors are like this, infact most arent, but there are a few that you really need to push to get them to do their "job" within the club, and this is where I can really see the benefits to the professional agencies such as PADI.
One of our best instructors recently left the club and became an IANTD instructor, but actually runs the courses at a discounted rate for members of our club.
But as has already been said in this thread, as long as the proper techniques and theory are taught, then the result once the training is complete should be similar, regardless of the agency, and also experience is important.
On the other hand I'm looking forward to my next lot of dive training, to become a Royal Navy diver, should be fun, and lots of hard work.