My .02 cents.
I've owned both, tried both, and like both. Add in Grim Tales, and we have three really cool systems that can emulate much of which any three can play.
If.... Spycraft 2.0 had been named Moderncraft 2.0, or just Moderncraft, then we would not be having the discussion of saying Spycraft 2.0 is primarily a "spy, espionage" game. When I think of Spycraft 2.0, I think of it as Moderncraft instead.
With the campaign qualities in the back, and the conversion documents on their forums, including the psionics and magic stuff, then it's easy to play a supernatural game using Spycraft.
I prefer to play d20 Modern more for one, and only one, reason... the way I run my campaigns, I like the Wealth system more than the Gear picks in Spycraft. I don't run mission style games myself, where people can choose to pick what gear they want for missions. That's not my preference, and so I will stick with the inferior game system simply because, for me, that's way easier for me to handle.
If you guys came up with a NON-GEAR-pick-selection system for equipment, for the classes, using a variable Wealth mechanic like d20M instead, then d20 Modern is history. Period.
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On a SIDE Note: When are you guys coming out with FantasyCraft? Huh? C'mon, I know you are thinking about it. Lots of people have been asking, off and on, over the years since Spycraft first came out. What's taking you all so long?