(1) Introduce the "Team Error". When two or three fielders surround a pop fly then let it drop because they cannot communicate decisions, the batter does not deserve a double, and the pitcher does not deserve a potential earned run.
(2) Pitchers' errors should not reduce their earned run averages. Let the pitchers pay for crappy fielding with earned runs. When a shortstop boots a grounder, that is not the pitcher's fault. When a pitcher throws the ball into right field rather than to first base, that is the pitcher's fault.
(3) A fielder should not be spared an error because he does not get to a ball he should get to. For example, if an outfielder fails to catch a fly because he gets a lousy jump, his first move is in the wrong direction, and he doesn't run fast enough to compensate, is that really less an error than if he gets to the ball but lets it glance off his glove? Yes, I know it's hard to make a judgment, but that's why we pay official scorers.
(4) When a rookie (say, Howie Clark) lets a ball drop in the infield, because A-Rod as a baserunner yells, "I've got it," A-Rod should be ruled out, and the rookie should have the right to kick A-Rod's a$$ around the block.