The Confederate States of America were established on a platform of a lack of centralized power. This new nation promoted the individual rights of states. In doing so, the Confederacy lacked the ability to do many things as a whole.
The Confederacy had difficulties raising the money needed to fight a war on a large scale because they could not levy most taxes. In protecting the rights of states, they created a government where little could be done on a national level. A Supreme Court was not established, and therefore no one could overrule decisions of individual states.
The new government of the Confederacy did grant more powers to the executive branch, though they established a term limit. As the war progressed, the government became more centralized out of necessity. They started to control the railroads, as well as harbors and rivers. They began to control production of goods. The government also began to tell farmers what sorts of crops to grow in order to support the war effort. This angered many farmers who had previously enjoyed a high level of independence.