Just a few things to trigger some thought and discussion. I of course have no insight into mission design at all...
1) Purpose. What is the difference between a "Mission" and an Order a squad leader gives his squad? Things like "attack a generator" could easily be done with a squad waypoint and a voip/text message by the squad leader. Simple and effective, and very flexible. What makes a mission special? What is its purpose vs squad-level command? What do YOU think its purpose is?
2) Scope. What is the purview of the Mission? Is it to get a single task accomplished? Is it to provide general direction to your empire? Is it to communicate needs and desires?
3) Scale. How many missions do you expect there to be at any given time? Too few and they may be overwhelming response or simply completed too quickly. Too many and most will go unaswered. How do you solve "mission creep" where over time more and more missions appear? We saw a lot of CR5 creep in PS1, so things like cert gates do not achieve a stable rate/number of missions. What do you think is a good Mission-to-player ratio? 1:10? 1:30? 1:50?
Three important questions when talking and thinking about missions. How do you see the answers as a mission creator vs a mission recipient?