This is generally due to the ownership structure being different in MLB versus MLS. MLS is centrally owned so the league can easily make whatever deal it wants

This is generally due to the ownership structure being different in MLB versus MLS. MLS is centrally owned so the league can easily make whatever deal it wants for broadcast rights. MLB isn't centrally owned and therefore the goals of the league are often in conflict with individual owners. The owner of the Yankees doesn't want MLB.tv to devalue the Yankees' investment in the YES (Yankee Entertainment and Sports) Network for example. That leads to complicated rights in which different entities own different pieces of the broadcast rights. Once this system came into place, it becomes incredibly difficult to unwind because there are now hundreds of media contracts between dozens of different entities. They can't just introduce an all-inclusive MLB.tv without breaking a lot of those contracts and they can't just wait until those contracts expire because they all were signed independently and therefore have their own timeframes.