Honestly, I don't like Spycraft 1e and I like Shadowforce Archer even less. Out of the box...er, book, what I like about Spycraft 1e are wounds and vitality (however, I prefer borrowing some options from the 3e D&D Unearthed Arcana) , Armor as DR being default, its handling of Action Dice, and mission based XP. I even like several of the Weapon Basics and Martial Arts Basics feats. To be honest, I don't recall how Spycraft 1e handled automatic and short burst fire (probably, better than the mechanics for d20Modern). My big turnoff to Spycraft 1e, however, is the classes (and I know for Spycraft 1e fans it is the reverse). I have a strong preference for the Feat and Talent approach of d20 Modern classes to the Spycraft classes (even if I do not like one of the d20 Modern Tough class's Talent trees).
In addition to not liking the Spycraft 1e classes, I dislike Spycraft 1e martial arts beyond the various Basic Feats. For myself, the wire-fu/wuxia focus/feel of martial arts in Spycraft 1e (which the designers state in the rulebook is intentional), is a major turn-off. I also found the Shadowforce Archer Martial Artist class to be a major a disappointment for what I want. While, it is an extra purchase, for d20 Modern, I vastly prefer Blood and Fists from (RPGObjects) both in how it handles martial arts and martial artists. Depending upon the "dials" used, I feel it allows for a wider range of martial arts portrayals as seen in television and movies and just does distinct martial arts styles better.
The above stated, my preference for Espionage would not be either. I would turn to Bond 007, Top Secret SI, Savage Worlds (with the Agents of Oblivion book), or even either GURPS or Hero System. As for modern or future gaming in general, there are several other systems that I would choose before a d20 class/level system, but, as I wrote in an earlier post, I could use d20 Modern if a group really wanted a class/level system.
.