For me, that'd be a multiplayer war sandbox. Take a big map, plop down resources, population centers and factories, spawn a lot of players who then have to organize to fight a war.
- To add espionage, you'd not hard-code a lot about the way teams organize(think removing the guild mechanics from WoW), so one could sign up with one side, then run to a different side (who do not know you already signed up with the first) and do ye olde double agent.
- Research could be modelled as being done by NPC civilians, which produces documents detailing the results. These documents must be on-site whenever the research is being used (i.e. present at factories), so it could be stolen.
- No need to go factorio on the production chains. Their purpose is mostly to enforce cooperation to reach better hardware for the guys in the field.
So, what's your crazy dream game that's never going to be built?