Keep in mind a lot of various and regional changes happened early in baseball's history and that baseball as a professional sport is much older than football or basketball.

Ground rule doubles were briefly home runs in some leagues, foul balls once didn't count as strikes, then you could strike out on a foul ball, intentional walk changes, spitballs outlawed, balk rules ...

Baseball was probably just as fluid in its first thirty-forty years as basketball, it was just a long time ago.

Edit: Another big one was the pitching changes in the 1960s after a wave of pitching dominance: http://www.baseball-reference.com/bullpen/History_of_basebal...