Why do Maeda Jun productions so frequently feature baseball?
The two reasons I can come up with is that Baseball is one of the most popular sports in Japan, and therefore is a common troupe in anime and Maeda Jun just uses it a lot, in order to provide a filler and some comedy in a show.

The second reason is advertisement for Yokohama DeNA BayStars, where they collaborate on the baseball episodes, where some characters are based on or named after the DeNA team members. But, I can only be sure for that for Charlotte, not the other anime you have mentioned.


  This entire anime is done in collaboration with DeNA Baystars, which is a baseball team in Yokohama, Japan. The characters are even named after the team members.