Pitching is key in baseball, as anyone who plays the sport knows. I recommend upgrading your pitchers before you upgrade your players. If you have a pitcher who can go five innings and only give up one run with regularity, you're pretty well off.
First thing, you have to find the three of your five pitchers who have the most maximum points. Start upgrading these three pitchers. The most important categories to upgrade are stamina, drop, and either left or right curve, whatever the pitchers throwing hand is.
Stamina is so key, I cannot possibly stress it enough. Even the biggest workhorse in Baseball Stars can only eat up about five innings, so you'll need two of your three pitchers to have 13+ stamina points. I'd give the other one about 5 points. We'll get to this guy later, but for now we'll focus on the other two.
Hopefully one of those pitchers is a righty and one a lefty, but if not that's OK. The next big thing is drop. Give each of your two pitchers about 12+ drop points. This gives them a very good chance of their drop pitch actually dropping.
Your pitchers also need a curve. I would say about ten on their throwing hand side, and about six on the other. This will keep batters on their toes.
Don't go in order, using your first fifteen points to give your pitchers stamina, your next fifteen to give them drop, and so on. Stagger them. If you get five points in your power up, consider something like two stamina, one drop, and one on both curves.
Now for the third pitcher. This guy will be your closer. He needs five stamina, fifteen speed, five curve on either side, and a non-existent drop ball. This guy's job is to come in for the last inning or two of a close game and shut the opposing team down.
When your rotation is built the way I described here, it should be virtually unstoppable.