When your mission statement is "simulate a galaxy", it's easy to let your imagination run away with you. I certainly participated in my share of grandiose concepts, some of which ended up in the game and some of which were justifiably killed off at various stages in the process." And in fact, that mission statement inevitably introduced new concepts, some of which brought the old thrill back, and some that aggravated many loyal fans to the extent of pronouncing the game "unplayable".
In general MOO3 came out to be what most expected it to be - a gigantic space epic. The manual and the strategy guide could have been novels on their own - describing at large the events preceding the actual gameplay and creating a complete universe in Lord of the Rings" fashion for example. The number of planets rose to about 1,500 (average of 5 planets per each of the 300 star systems) from about 300 in the previous titles. The number of galaxy races vying for control rose to 16 and the level of customization gained depth and realism. That level of complexity somewhat shifted the human intervention in the game. In the first two games the focus was mostly on micromanaging the colonies - adjusting the day-to-day care of food supply, mineral harvesting, technology research and so on. In MOO3, that task was appointed to newly designed "planetary viceroys", AI (artificial intelligence) servants to take care of day-to-day tasks, while upon the human player was appointed the task of macromanaging the empire - dealing with diplomacy, spying and waging war campaigns. That is the one of the main reasons for some fans to complain. They are not against the concept of viceroys but rather against the inferior AI which actions in some cases don"t make sense. However, that is not true. The emperor has the power to implement development plans which in broad limits outline the tasks for the viceroys. For example, you can specify that mineral poor worlds develop manufacturing, mineral rich worlds develop mining, frontier planets build planetary defenses and so on.