Not really a wish, 'cause I can see this is the tendency from Fantasy Craft, but I really hope you'll continue to keep things simple and go to the essential. I'm thinking of a few main points where it is an absolute necessity:
Dramatic Conflicts: Though one of my favorite aspects of the game, they tend to be a little too complex. Too much choices, too much restrictions (chases on foot are extremely limited for example), too much intricate additional rules (smash points, gah!). On the other hand, a lot of various effects (crisis, stress, etc.) is good.
Weapons: By far, the point that needs to be cut the most. Real-world weapon is cool, iconic espionage weapons is even better, but a 2-pages catalog for assault rifle is IMO useless. 10 to 20 iconic assault rifles should be well enough. Same thing for guns, etc. Who cares if the bad guy has a Glock 17, 17L, 18, or 19?
Actions, conditions, etc: I love how you've condensed these parts with FC, so I guess there's no fear to have here.
NPCs: Too many qualities IMO. FC is a great effort of condensing those, but I think that without the fantasy element, they can be even more condensed in SC3. Again: Keep. It. Simple. Strongly thematic, effect-based qualities, maybe a separate section for animal qualities, and that's it.
Gadgets: Too many choices in SC2, making it the king of all item categories by far. OK, that's what it's supposed to be, but then it shouldn't be considered equivalent to other items. Should you make it something as distinct and unique as magic items in FC, it would be great.
There are other things I would like to point out, but maybe later. That was my "lets cut down Spycraft to 400 pages" post.