The issue with 3 at the back is that you end up having almost redundant players on the pitch. With most teams now only playing with one out and out forward, you end up with one more centreback than you ordinarily would.
Even when teams played with 2 strikers, we had that same problem under Evans.
It also means that, depending on how good your wingbacks are, that the wide forwards can get a lot of time and space in the gap where a right back would be. It's similar to the issues we had when a space opened up behind Trent when he went forwards.