I don't think there's a right answer for how many teams should make the postseason. The main reason for the play-in games in the NBA is to avoid tanking for high lottery picks (like the Lebron's and Wemby's of the world), though with the amount of parity increasing, lottery picks may not matter as much as they once did which could make the play-in games a bit "extra".
As for baseball, I think it's fine as-is. I certainly thought having only 2 from each league make the playoffs back in the day was a little weird, but maybe 4 was good enough. That said, if you get swept in a best of 5 after having a small break to rest aches and pains (which any athlete would appreciate), then you're just not ready to win it all.