Missions need improvement.

Imagine an assassination mission where you had you use your Conceal to make it all the way to your target unnoticed, kill your target, get the reward and then try to make it out alive.

Right now assassination missions are just kill everything you see. If it moves, kill it. There's a difference between mass murder and assassination I feel.

Missions that had mult-parts: You choose a mission. You then set up the terminal to choose another mission and the server checks to see if you already have a particular mission chosen. If you do it gives you the continuation of that mission ... up to a total of three parts.

Missions that had political ramifications: say Funcom kept track of how many types of missions were being performed and this somehow affected their storyline.

Just some ideas...