Why do Maeda Jun productions so frequently feature baseball? Things by Maeda Jun feature baseball. A lot. 

Episode 1 of Clannad: After Story is a baseball episode, and there's a fair bit of baseball elsewhere in both seasons of Clannad. Episode 4 of Charlotte is a baseball episode. Episode 4 of Angel Beats! is a baseball episode, and the whole Hinata/Yui thing later in the show is also rife with baseball. Little Busters! is brimming with baseball. I'm told that Rewrite (the VN) also has baseball in it. Dunno about Air or Kanon, but I'd be surprised if they were devoid of baseball. 

I know baseball is big in Japan, and I know that Maeda's work is formulaic to a degree (ever seen the Maeda Jun bingo board?), but this goes beyond that. Why does Maeda Jun put baseball in so many of his works? (I've heard that Key has some sort of sponsorship deal with a baseball team. Is this true? If so, that'd explain it.)
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.