I have used both and like both.
4-3: Was my mainstay for almost my entire GD career. Still is my Heisman D1AA defense. If you have the right players, it works great. Probably have to mix in some 4-4 and Nickel to cover the full spectrum.
3-4: I converted on my D3 team during the last season of 2.0 and had great success. I had a "co-coach" under another ID who fielded great defenses using the 3-4, so I decided to try it out myself.. I do NOT use any other defenses. It is 3-4 in ALL situations, against ALL formations. Had pretty good success the first season of 3.0.
I agree with helgi on 3-4 flexibility. I also play against him with it at D3.
Bottom line: I really think you can make any of the defenses work if you recruit for it and learn how to use it properly.