The Benefit
Making use of the Zeus module in conjunction with community made addons such as MCC can prove to be extremely useful when trying to create a mission that is dynamic and involved for those that are participating.
The Problem
From what I've seen a lot of people that want to get into the Zeus mission making tend to get too excited and try to overdo a mission. What they dont consider is the decision making process that the players implement when deciding how to complete a mission. It's best in most zeus missions to keep it simple, or as the saying goes "Keep It Simple Stupid." It may not seem like it'll be fun but as the game master you are there to provide the entertainment to your players and they will thank you greatly for this.
Desigining the Mission
A problem that I have often run into is that when doing Zeus missions often that players tend to not know what they want to play. I'd usually ask what they want to do for the mission and half the time they just make something up and the other half of the time the just ask me to give them something. So the majority of the mission design relies on the game master in day-to-day operations.
A good practice to put into play would be to have a campaign planned out for yourself that you implement for the players. What this allows is for you to be better prepared to create a mission which results in minimized preperation time on your part. Also it allows the players to anticipate the upcoming missions and make plans for the mission.