Things you want to do in a spy game depends on the kind of spy game.
I've run Bond/Alias style superspies using Adventure! and Bourne/Q&C style action thriller agents with uncinematic Unisystem, and played the former back in the day with Top Secret / SI.
The former is certainly easier to do, being a modern SF superhero adventure story with tuxes instead of costumes. The latter needs rather more thought, a coherent-ish plot and some knowledge of real locations and the like. It's probably closer to Vampire without the, well, vampires.