Honestly reffing across the league just drives me crazy. How many times a season do the refs influence games? I don't think it is intentional by any means but it happens to at least two games a week. I think there are two things the NFL could do to fix it and fix it rather quickly.
1) Do not let refs off the hook when they make bad calls. It happens all the time, ref makes/doesn't make a call in game, league reviews its later and says the ref was wrong. What ever happens to these guys when they are wrong? I don't have a good plan but something like fines or game suspensions may make refs try harder to not influence games with incorrect calls.
2) This is the easiest by far. Allow all plays (penalties included) to be challenged by coaches. Coaches will not challenge every penalty but game changing ones would be challenged. If this was a rule and today Pagano challenged the Luck fumble when Clemons hit Luck in the head, it would've sucked but it would've 100% been the right call. The push off by Wayne in the endzone also would have been caught by a review. It would not add tons of time to games because coaches would have the same amount of challenges but it would definitely help out in reducing the role the refs can play in games.