Agreed. I haven't sat down to try and perfect it, they don't pay me enough to do that.
One part of it is quite easy. Every position gets paid a base amount and beyond that everything is earned by each player, during each season. Due to technology and todays collection of just about every tidbit of information that happens in a game, statistically and logistically it probably would be quite easy to do.
The difficult part is how do you regulate it in relation to a cap and trying to continue to keep all 32 teams on a somewhat equal playing ground to keep the league competitive. Teams could sign the top 11 players on offense at that base rate and at the end of the SB win say "oh crap, now we have to pay for it, but it was worth it". Of course, if TD's and yards are part of the pay scale, a team can only total of so many of those in each game, so the wealth is spread around.
The current pay system is mainly based on "predicted value". Sure would be nice to bring in more of a pay system that payed on "Actual earned value".