Most of those aren't the reasons baseball changed the rules. The game evolved, and MLB is encouraging things it wants to see.
Stolen bases dropped because teams figured out they weren't valuable if you got caught. So MLB made it easier to steal, thereby encouraging teams to steal more.
The three-hitter minimum was put in place to reduce game length, full stop.
Pitchers never hit, can't forget something you never knew. So baseball mercifully put an end to that fiasco in the name of making the viewing experience better.