At the risk of asking for things already mentioned, here's my personal wish list based on my experiences running 1.0 and 2.0 in play-by-post and tabletop and fiddling with FantasyCraft:
Keep It Flexible
I have no real fear this will change, but its worth mentioning - the main appeal of Spycraft for me as a GM was its ability to stretch and encompass a variety of modern action-adventure subgenres. I think I can also say my players liked how customizable their PCs tended to be. Talents, Specialties, the wealth of useful Feat choices, and things like Campaign Qualities are all gold.
Make It Easier to Learn
On the flip side of the previous point, it was common for my players to get overwhelmed by all those options and features. They aren't neophyte gamers, but 2.0 flummoxed many of them. Since a lot of the rules seemed integral to the game, I was reluctant to simply excise them so I tended to spend a lot of time trying to explain the interior logic of the choices and give examples of what each thing would mean in gameplay. Perhaps some "quick start" PCs or tutorials would be useful in giving folks guidelines?
Repeat What Bears Repeating
One thing I noticed in FantasyCraft was that some bits of vital information would be mentioned once and then never mentioned again. While I realize you guys were probably wanting to avoid excess text given the size of the rulebook already, some redundancy on critical features wouldn't hurt. One of the big examples I can think of is the rule regarding starting skill point totals for PCs at 1st level. This is given almost in passing in one part of the character generation chapter but not repeated in the classes stat block. Given that, in my experience, nobody spends the time to read the entire character generation chapter in detail when making their first PC, repeating this kind of thing in places where its necessary would be helpful.
For the Love of God, Fix The Gear Rules
I think FantasyCraft pointed to a sea change in how you looked at gear, but I just want to be clear about this: gearing up in SpyCraft 1.0 AND 2.0 was a nightmare. Even if I included options to simplify it from the Big Score, my players would spend long periods of game time on trying to grasp what all those codes meant and what upgrades they could get and what precisely they needed and then I'd have to track special qualities and flip pages to figure out how X interacted with Y and...well. You get the point, I'm sure.
I'm personally not all that interested in detailed lists of equipment - and while I realize some players like to dig deep into hardware even my tech-head, NRA member, min-max loving players would get confused and annoyed by these interlaced gear systems and subsystems. The game is really about what the characters do and how they interact with the obstacles I present them with, NOT whether or not they picked the optimal armor, weapon, vehicle, or kit for the job. I'd personally suggest that if you want to include lots of specificity and qualities for each and every bit of non-living equipment that you make it more optional and maybe even in a Gunbunny-friendly sourcebook rather than in the core rules.
Be Careful With Gadgets
On a similar note to my previous plea, I'd like you to be more cautious when it comes to gadget rules. While I realize its partially the GM's job to spot when a player has abused a given system, 2.0's open-ended gadget options could quickly go from "that's cool" to "that's totally ridiculous and unbalancing". Things like Skill Boost, for instance, would often result in PCs who had no Computer skillz but who could defeat any Hacking challenge provided they spared some gadget slots to get a bunch of limited use +10s to their skill checks. This was especially grating if we had another PC WITH Computer skills but whose player was less system-savvy and couldn't keep up with the min-maxer. Ultimately, I ended up having to lock out practically every gadget rank in PBP games because of this.
Dramatic Conflicts Should be Fun
One of my favorite aspects of SpyCraft in any version was the idea that car chases and computer hacking could become featured set pieces of their own in Dramatic Conflicts. One of my least favorite aspects of SpyCraft was the way these conflicts could become bogged down in interminable fiddling. This was especially true if the conflict was focused on one PC doing everything (see: Hacking) and/or if the conflict featured a lopsided contest. In the former case, the other PCs would have to sit around and wait for the guy to do his thing - which was often a predestined outcome that wasn't that engaging - or the players would end up having to pick one or maybe two strategies since they couldn't qualify for anything else. I ended up abbreviating many would-be conflicts into simplified Complex Tasks, which is a shame given how excited we were about Dramatic Conflicts initially.
If Dramatic Conflicts aren't being dropped or made into something totally unrecognizable, I'd suggest reviewing the DCs, the skill bonuses of probable participants (PC and NPC alike), and how involved you want to make given Conflicts in the future. I'd also be wary of offering one min-maxed specialist PC a system that lets him hog spotlight time, stay safely at home, AND seemingly solve numerous problems (Hacking, I'm looking at you again). I'm okay with letting them shine from time to time and be an asset in an adventure, but when they're doing the work of an entire team on their own with little sign of breaking a sweat, something's wrong.
In A Skill-Focused Game, Skill-Focused Classes are Paramount
One thing I noticed with some alarm was how experienced SpyCraft 2.0 players would almost always multi-class into Scientist when trying to get the best bang for their buck. Once I got past being literally minded about what the class represented, I was still left with the sensation that it was a class that you'd be STUPID not to take given what it offered. I don't like this, personally; it suggests that theres One Best Way to do something in the game (i.e. Get High Skill Bonuses/Big Threat Ranges) that seems to be pretty crucial to the default genre. While I realize that character classes like the Soldier are meant to be balanced by virtue of having all those combat Feats, the fact is that skills were always more relevant and potent - especially in a modern setting that features investigation, interaction, and intrigue.
Looking at the Scientist equivalent in FantasyCraft (Keeper) and what changes were made, I think its probable the designers noticed this too, but I still felt obliged to mention this. Skill Power = Power in SpyCraft, and this is especially true if Dramatic Conflicts return in 3.0.
Making Bond or Bourne Should Be Easy and Obvious
While I realize that Bond and Bourne aren't team players and therefore may not be the ideal models for PCs in a team-based game, I still think it should be fairly easy for them to be statted in 3.0. I never got totally convinced this was the case with 2.0, as the results often were weird multi-classed hybrids. They're archetypal, particularly given the 21st century take on the genre, and even if a PC version needs to be less omnicompetent in a team context to protect niches, I also don't think they'd need to be complicated or overpowered to work.
Same goes for just about any appropriate spy genre archetype, ideally; Smiley, Nikita, Modesty, IM force characters, whatever - it should be made obvious to GMs and players alike how you might use them as a model and what class suits them best.
Skills are clearly central to SpyCraft, and I always liked how they could do a variety of things in previous versions. One thing I didn't much like, however, is that they didn't seem to be scaled very well. Networking was one example, what with its wacky DCs for summoning contacts, but there were others. FantasyCraft looks like it addressed some of this disconnect, so I'm hopeful 3.0 will do the same for SpyCraft.
On a related note, though; Blend/Sneak, Notice/Search. I get the idea, but I still don't like the way they're implemented. As a GM, I'd have to track bonuses, roll for players, and get confused about when which applied. I'd also get perplexed by if/when you could use action dice with them, activate threats or errors, and what precisely those would mean. Then there's the issue of what successful use meant, how long it'd apply, how a sneaky person could be obvious (high Sneak, low Blend) or an alert person oblivious (high Search, low Notice), and how that related to NPCs. And my players - always confused by them. Its just too much nebulous vagueness for something that's fairly crucial and common in a spy game, I think. Could you consider conflating them or else using something like D&D 4E's fixed passive skill checks? Or, at the very least, could you explain them in clear and concise ways so everybody gets how they're supposed to work? Just a thought.
Minions, Villains, Adversaries, Special, Standard, Mastermind, Lieutenant...
FantasyCraft introduced the Mook NPC quality. It also apparently lowered the Damage Saves of yon Standard NPCs so they weren't as bulletproof as those in SpyCraft 2.0. This is something I hope carries over to 3.0. Having said that, though, one thing that always got weird for me when working with NPCs was getting the definitions down pat. There are places in 2.0 and FantasyCraft where we're told that there are two types of NPCs (Standard and Special), but later on we're also told there are kinds that are unique because they oppose the PCs. Then you get NPC qualities that sound sort of like they are even more subtypes that have special roles - often simultaneous with the other categories.
All these years later, it still confuses the Hell out of me, especially because many of these mentions are only made once and never again. Antagonists? Adversaries? Villains? Masterminds? Lieutenants? Minions? Foils? Augh! I hope this is clarified a bit in 3.0.
Take Your NPC and Shove It, I Ain't Tracking Him No More
FantasyCraft did a lot of neat stuff to make the Crafty engine easier to grok and work with. It did, however, do one thing that made me fear for my sanity in running it. This is the notion of PC created/controlled NPCs with their own roman numeral-laden, NPC quality-having stat blocks. Which level. And change. And somebody has to sort out at the game table using the NPC chapter.
I know, I know. A good player will be sure to take care of this on their own, preferably before/between sessions. But, man; that's just a whole new level of crunch for me to instruct my players about if they decide to have a Personal Lieutenant, Animal Partner, or some mysterious minion-summoning class or Feat ability I have yet to comprehend. Do people really play with these PC-controlled-NPCs that much? And is there any way we can make it simpler for us GMs to work with them? 'Cause, right now, if I see them in 3.0 as they appear in FantasyCraft, I'm going to probably get an ulcer and redact their mention with black blocks. But that may just be me.