I recently ran Spycraft for six months before my group and I gave up on it. It is a great game once you get everyone to learn it all, but it has a high barrier of entry. My group never cleared that barrier. If I were to do it again, I'd introduce the system very slowly, adding more complexity with each session. And I'd have a lot more precampaign discussion about what kind of spy game you're running, since modern espionage covers a lot of ground. Also, I'd know the following:
First, get the errata. There have been many updates and revisions since the game came out. The errata is long but complete, and they do their best to fix whatever problems were introduced.
The Gearing Up phase of Mission Startup is the single largest problem with playing the game. The equipment and gadgets lists are immense, and you can spend one, even two sessions just having players learn the gear options. This problem is partially solved with bundles (pre-built packages of gear), but unfortunately the bundles are spread over the entire book line (instead of just one supplement), and include gear introduced in those books. If you poke around online (shh!), you can find typed up Bundle Cards (for printing, obviously), and then simply make up the gear you don't know about. I strongly suggest that you have a list of preferred equipment ready for the players for their first mission. Don't even let them near the book. This problem will likely lessen somewhat if you stick with the game long enough for the players to get a feel for most of the gear, although it never did for us.
A side effect of the lengthy Gearing Up phase is that each mission should last a few sessions away from home base, to minimize the time between Gearing Up phases. If the agents can come home and restock, you're just compounding the Gearing Up problem.
Combat is pretty fun. If you know d20, you'll do fine, as it's an improvement over base d20 combat. Avoid autofire, though, as it's weak and doesn't model what most people think it will. It's less effective than 3-round bursts.
Most of the core classes are severely misnamed and give the wrong impression of what purpose each serves in a group. Of the six core classes:
- Soldier and Wheelman are correctly named; but know that some people feel that a Wheelman is frequently as tough as a Soldier.
- The Pointman is actually the versatile teammate/leader, not the guy you would send to lead the way into combat. (avoid this class, it has a few pages of errata just for it; it's like a base class for advanced players)
- The Faceman is three parts master of disguise and only one part confidence man. Some of its class abilities can break stories if you're not careful, like Cold Read.
- The Snoop is actually the team nerd (computer/surveillance expert), not a skulking sneak or man-in-black type.
- The Fixer is actually ten parts D&D Rogue (sneak attack, evasion, uncanny dodge), and one part black market contacts.
Be clear with your game group about these roles, and tell them to ignore the class names.
If you're familiar with D&D encounters and how to set up combat challenges for a party, then ignore the Mastermind system. It's really cumbersome and you end up basically at the same place anyway, except without hours of number crunching. Boy, did I learn this the hard way.
And you don't even end up with statted NPCs!... you have to do that by hand anyway. Read the examples, and see what they recommend, then wing it.
Reread AscentStudios post on the subsystems. They are complex and difficult to bring across to new players. Action dice can be spent at least five different ways, so have a cheat sheet ready for new players.
Finally, dump the Disposition system and its related feats. It's really unwieldy and a time-killer to use in play. When 4 PCs meet one NPC, that's four Disposition checks. For three NPCs, it's twelve! Repeat for every NPC, every mission you meet them, as their disposition changes across missions.
Oh, and if you can find it, buy
Most Wanted by Paradigm Concepts, which turned out to be the single most useful supplement for actually playing. It's just an NPC book, and so only for GMs, but it comes with great villains/henchmen and can save you a lot of time.
Good luck!