Another possible way to implement a highly skilled (but otherwise mortal) character is to go the Jason Bourne route. Give up the +2 refresh bonus for being a pure mortal, take beast change to represent the change between your 'killer' self and your 'normal' self. This lets have two different skill sets, and switch between them as needed. This also lets you get a bunch of minor cinematic powers.
So we could have something like:
Regular, stealthy you:
+5: Burglary
+4: Deceit, Fists
+3: Endurance, Presence, Rapport
+2: Alertness, Empathy, Investigation, Scholarship
+1: Athletics, Conviction, Discipline, Guns, Stealth
And then, assassin fighty you:
+5: Fists
+4: Alertness, Guns
+3: Burglary, Endurance, Presence
+2: Deceit, Empathy, Investigation, Scholarship
+1: Athletics, Conviction, Discipline, Rapport, Stealth
And your refresh total might look like:
Powers:
-1 beast change
Stunts:
-1 footwork
-1 lethal weapon
-1 medical training
-1 no pain, no gain
-1 languages
Total: -6
Leaving you with 4 points of refresh left.
You are pretty tough, you have great or superb basic defenses, have a lot of utility skills, can still fight ok for a mortal, speak up to 5 additional languages, can do medical treatments at good skill. If you want, you can also stack up some minor powers, which are generally more effective than stunts. For example, you could replace lethal weapon with 'Dim Mak' and have a hacked version of incite emotion that relied on fists instead of deceit. Then you could do instant blocks against people at fists +2 and justify it that you are hitting the chakra points and immobilizing them, or something. And you can take cloak of shadows and rename it something like "student of batman". Or you could take 'hollywood hacking' as a minor power, probably similar in implementation to psychometry. And as far as everyone in the world is concerned, you are just a regular mortal.