Eisen makes the point clearer than I have that I think a lack of communication has allowed some of these bad calls to stand. Communication shouldn't end after pre-game, and everyone on the officiating team ought to feel comfortable with saying to another official "Are you sure?".
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Hell, on that flop of a RTP call in the Dolphins-Eagles game, you can see the whitehat ask his umpire "Are you sure?" clearly, and yet they still went with the wrong call. They need the replay official to jump in and say "Don't call that, it's not a foul!"
There should be more than one replay official. Also, they should get to call anything, and they should also tell officials on the field when they're wrong to wave off bad fouls. It's absurd that we can put someone in a booth with access to all of the cameras (and instant replay), and yet can't give that person (or people) the ability to correct 7 guys who are relying on only their own eyes in real time.
If this results in too many penalties called, then either players need to get better at not breaking the rules, or we should fix the rules to not have as many things be penalties.
It's not that people hate replays, they hate that it slows down the game to a crawl. We have the technology, and the NFL has the money to have short quick replays from above to get the call right and not take 4 minutes.