ROFL! Nice one Glim.
As to the master plan, all I can say at this moment is that the ideal template is "Burn Notice full of Bond," by which I mean the team focus and composition of Burn Notice with Bond as a template for individual agents (and then, most specifically Craig-era Bond).
I've never personally seen the need to equate levels and advancement with linear story progression - I think you can play through pretty much any story at pretty much any level and playing "globe-trotting superspies" at Level 1 is a great way to avoid ability saturation and option paralysis. I am, however, very much in the minority on that, and so we're looking at levels far more traditionally in Spycraft Third. As such, Level 1 agents will be viewed mostly as new recruits - fully trained and ready for the field, of course, but definitely not as experienced as their higher level colleagues and superiors.
We're also approaching this part of the game structure a bit differently this time around, but that's about all I can say on that for now. Expect an upgrade, I guess. I can say that as well.