Drew Brees tweets 3 rule changes he wants the NFL to make

To your last point. A possible solution would be to make repeated PI by the same player an ejectable offense. I.E. You have a DB that keeps dragging a WR down when he is beat, he gets away with a 15 yard penalty once, but he does it again, flagrantly, he's out. Obviously there is nuance here, and it may not be that cut and dry, but individual consequences would straighten some of this up. You could also impose fines on PI calls. Lots of ways to incentivize clean play without basically giving free completions. A penalty that results in a 55 yard gain is absolute BS.
Putting the game more into the control of the players is the ultimate goal.
This entails taking away from the refs some of their arsenal of penalties.
Football is a game of centimeters and milliseconds.
Reffing certainly has its challenges.
But that's why the game needs professional officials. Not in name only, but in the amount of time the referrees spend in training.