Kelly can't be on the floor without either Horford or Amir. He just doesn't function well as the only big on the floor. He's attacked in the paint by the opposing teams offense, and given the added responsibility of rebounding, blocking out, and protecting the rim. Not really his strong suit.
Zeller actually plays well with KO, leaving Kelly as a scorer, and playmaker. Zeller also gets wide open shots while KO is on the floor, while being the primary defender in the paint. In short minutes they work well together. While not being a very physical duo, both run the floor well and have decent pick and roll skills.
All while giving Horford and Amir a few more minutes on the bench.