Spycraft 2.0 is the better game. It's got some really innovate (for d20, and occasionally for RPGs in general) concepts and once you get used to the MASSIVE FREAKIN BOOK FULL O STUFF (not quite HERO 5r, but unless you're looking at ballistic armor, what is

), it plays well, too.
d20 Modern is easier, faster until you're fully used to both systems, steps outside the archtype box, and is much, much more flexible. Also, the small arms/melee rules are closer to both action movies and reality: Guns are easier to use and have range. Melee weapons require more skill (read, feats) to use well and do more damage.
Spycraft
+ Excellent use of the d20 rules
+ Models the major non-SF spy/action genres
+ Action dice are better than action points
+ Many innovative and useful subsystems
+ NPC generator
+ Expanded skills
- Harder to learn
- Slower until fully mastered, and maybe even then
- WP/VP
- Pointlessly complex initiative system
- Almost no 3rd party support
- About as compatible with other d20 as True20, maybe less
d20 Modern
+ Flexible base classes
+ Compatible with almost every d20 book you ever bought
+ By far the best 3rd party support around
+ Melee/small arms models most movies and real life better
+ Keeps 3.0 cover rules
+ Easy to learn
- Lacks innovative and useful subsystems
- 1st-party support tends to be magic-oriented
- Vehicles and heavy weapons are poorly handled