The reason everyone uses 3-4 is because it does so well vs. passing offenses. That way you can practice only one defensive formation instead of 4-3 and Nickel, allowing you to either practice it more or spend those minutes on something else. While I assume Nickel would work better against Shotgun, the reality is almost nobody uses Shotgun, and for the few teams that do, you might be able to just beat them with talent and 3-4 as has been mentioned.
I'm not very knowledgeable about defensive formations, gameplanning, etc., but most of the top coaches are using 3-4 so I'm converting all of my teams to that for the time being.