One thing one has to consider is the difference in main focus of the different vessels: The ISD is a jack-of-all-trades, combining the role of carrier, troop-transport and battleship, serving as the backbone of the empire's occupation-forces. As such they are built to last with an emphasis on high, but sustainable performance and endurance for a reasonable price and relatively easy maintainance. RebelAlliance/MonCalamari-ships on the other side are high-performers, built to defeat those larger craft, while being built on a smaller frame. As such the ISD would be a marathon-runner, while the MC90 for example would be a 100metre-sprinter, with higher need of maintainance and higher operational costs in comparison to the ISD (while probably being chaper to purchase). The RebelAlliance/early NR also has the problem of having no idea, what kind of fleet it wants or needs as a galactic power. As the RA it had to take, what it could get and as the NR it had to fight not only against imperial splinter-states with different levels of equipment (with Imperials like GA Thrawn having nothing bigger than ISDs available, while the DeepCore-empire had scores of Star Dreadnoughts and battlecruisers to spare) and of course the NR also wanted to be percieved as different from the empire. Hence, why we see so many different ISD-equivalents with limited production-runs, that also quickly vanish from the main lines of the fleet.