The advantages of the 4-3 are that it plays like a 4-3 should in real life. It is a straight forward vanilla base defense where the offense knows who the four players rushing are 9 out of 10 times. That last statement would be a disadvantage in my eyes. Another issue is only three LBs covering the middle of the field.
The 3-4 allows you to bring heat from all over the field confusing the QB as he never knows where the pressure is coming from. The main disadvantage of the 3-4 is that it doesn't play as it would in real life. What I mean by this is undersized pass rushing DEs can still do quite well for you. In reality you would pretty much want 300+ lb guys across the line whereas in Madden it isn't necessary.
Overall I prefer the 3-4. I attempt to keep my offline franchises realistic in regards to personnel so I tend to draft DTs to play DE and go for very quick LBs. I think having a fast LB corps can really add to the pressure you put on the QB as well as attack the rush with your big DL taking up blockers.
All in all it is a personal preference with the 4-3 playing as it should, and the 3-4 less so. I just like the creativity behind calling plays from the 3-4. I have also read that the Nickel 1-5-5 is a good formation for passing downs as it again can bring pressure from anywhere.
Check out this thread about people's opinions of the
importance of personnel.