The evolution of the Empire's fleet seems to be pretty well-established. The Old Republic, under Palpatine, commissioned the creation of a large space force from a coalition of Sienar Fleet Systems and Kuat Drive Yards, to be manned by the clone troops from Kamino. Over the next 20 years after the fall of the Republic, Sienar and Kuat continued to supply the Empire behind a position of neutrality.
However, the array of ships in the Rebel fleet have far less of a known history. Apparently the smaller frigates like the Nebulon-B series commonly seen were also Kuat designs, largely brought to the Rebel fleet by capture or defection. However, the big Mon Calamari cruisers actually outgunned older Star Destroyers, and were produced by the Mon Calamari themselves totally independently of any need by either the Old Republic or Empire. They are the mainstays of the fleet in the Battle for Endor, and though most are outgunned by the latest Imperial-II-class SDs, are still a threat. So, why would the Empire tolerate the existence of these ships, and of the shipyards to produce them? Wookieepedia states that while they occupied Dac, the Empire was unsuccessful in using the shipyards for their own means, but then, why not simply destroy them?