I too was having problems completing deep passes but Millenium's recommendation of barely tapping the receiver's button could not be more true !!! When I started doing this about a week ago, coupled with precision passing to the correct shoulder I started seeing more completions on the deep ball. Nothing over the top, but it does have a realistic feel to it. The last thing I want is a game where the deep ball is a money play the majority of a time !!!
This years Madden has the most realistic passing game of any game that I have ever played (including NFL2K5). At first I was getting frustrated with non-existent deep ball and passes over the middle. About 10 hours in practice mode helped me conquer both of these. My passing percentage is more believable now and I'm able to spread my passes all over the field.