There is a Mark Twain quote to describe this. "There are lies, damn lies, and statistics."
There are a lot of things that can go into those misleading stats. The head coach, the head coaches game plan. Not every coach gives free reign to their coordinators. In the end they are a slave to their head coach and that coaches philosophy.
Also you have to take into account your personnel. The 4-3 is a much easier system to run, you can plug in any professional athletes and run is reasonably well. There is less deception, less creativity, and its more players can run it. Especially since most teams starting from Pop Warner, to High School, and college have run the 4-3 in some way or another. They are more comfortable with it.
However the 3-4 is a much more complicated scheme, you have to have some vary specific things. You need to have intelligent players that can mask their blitzs and understand how to play well in it. Not every defensive player can transition well into it. You need some LARGE boys on the line. Especially at the nose tackle. and you need a big middle linebacker to take on blocks that will free up everything else. And you need talented pass rushing OLB. There are numerous examples all across the NFL when a team can't run a 3-4 well and them get embarrassed on D. There is no way around it you have to draft, teach, and pick up free agents that specifically fit the 3-4.
I realize this is excuse making on Fangio's behalf. I am not making a judgement one way or another on the guy until I see what he does with the Niners. Keep in mind the great Dom Capers failed as a head coach, as did his defense under his watch.
You look at any good coordinator and I will show you a year or a place where they failed statistically.
[ Edited by OX49er253 on Jan 9, 2011 at 11:18 PM ]