As far as replay, I would like to see them go to a system a little more like the NCAA replay system. Every play is reviewed, and the on field officials are notified if further review is necessary prior to the next play.
I also like the concept of having the replay official being the one to make the decision on the play, and just inform the Referee of the outcome. If there is any question on the call on the field, allowing the on field Referee to have the final say in the decision opens up some question as to whether or not he gives the benefit of the doubt to his crew mate when there isn't "clear and concise" evidence to change a call.
They also allow for replay to take a look at the "targeting" penalty, as in the college game it is also an ejection in addition to the 15 yard penalty. If the call is found to be made in error, (as to the targeting and illegal hit to a defenseless receiver) not only is the ejection retracted, but this year, so is the 15 yards.
There may be a way to review certain penalty calls, (roughing the passer being the most obvious) and have incorrect calls like the one on Eugene Sims in the Dallas game overturned. But to use replay to call penalties that are not called on field just isn't practical. The games would last 5 hours.