MLB Pitching Regulations

[SAump]

MLB umpires are tossing out perfectly good baseballs.
This was not the case when MLB umpires did not remove these baseballs from the game.

1) What indications should an umpire look for when deciding to remove a baseball from a game?

2) Can the defense, the pitcher, or his coach insist on getting a "good" ball back into the game?

3) Where are these rules or guidelines?