"Stole Fees" are not universal.  Many dioceses have done away with that.    

The wedding and funeral "fees" are due to the fact that organists and staff have to be paid who "work" the wedding or funeral--especially if it is on a weekend.  Does not justice demand that the employees get paid?  But those fees are not universal either.  It also depends if the parish has a cemetery.  People have to purchase plots.  

The fees do not belong to the pastor.  A small portion goes to his stipend--but the bulks of the fees goes to pay the cantor and organist.  Qualified musicians are expensive, sir.  Like I said, however the practice is not universal.  You will tend to see the fees more in the North East, less in the South.  However, if a person is poor, the fees are often waived.  

As for John 3, how does it present a problem for Christian Baptism?    Only a Scripture Scholar or lawyer would try to claim that the passage does not refer to Baptism--because they often miss the obvious.