I guess we'll have to agree to disagree on this point. I found the spoilers for City of Heroes - which was otherwise a miserable experience - to be far more helpful than they were problematic.

The main driving force for fps games played online as well as I would imagine for MMO is the player versus player competition. So what about some kind of spy versus spy system?

Each player is a spy, and starts with some captial and skill from the skill list. While the core of the gameplay revolves around competing against other spys. Rather trying to directly kill other spies, players try to out think each other. By building Spy versus Spy style traps using base components. Players get money from stealing it from other players and npcs as well as perhaps some kind of mission board. The mission board would be a place where nps and spies can post jobs they need doing as well as the fee offered for the job and a duration in which the mission most be completed in. The trick is of course you never know who your working for.

Skills would allow players to perform new task and the player would pay for training at various spy schools for these skills. For instance demolotions allows the player set and defuse explosives, and the expert demolotions skill would allow the player to build explosives.

The actual gameplay however would all be done through player based skill in an ever expanding array of mini games.

There would also be a reputation system. Well I think it would be fun and it focous entirly on in game content.