Hi! I finished (and won!) my first game of Subterfuge over the weekend, which means I'm an expert now. I probably won't be able to play again until August, so I figured I'd get these thoughts out before I forget them.
I should probably preface this by saying that I loooooooved the game, and the specialist system in particular was way more exciting than I expected. Most of the suggestions below are pretty minor, and I think everything is close to perfect as it is.
Anyway, here are some opinions!
• There are too many improve-combat-efficiency specialists: Lieutenant, General, War Hero, Thief, King, Engineer, Infiltrator! They differ in whether their boosts are flat or percentage-based, and which combats they operate in, but those differences don't feel big enough to justify seven different slots. If you're looking to cut out some specialists, I'd start there.
• I agree with previous comments that a specialist FAQ would help, but a little in-game diagram might be more effective. Double Agent in particular was confusing to me (the description makes it sound like the subs swap specialists, rather than the specialists swapping ownership), but a before-and-after picture would clear it up entirely.
• Okay, what's the deal with King? He sounds awful. One of my allies explained that he can be helpful in the very late game, but I think I'd prefer specialists that might be useful at all (or most) stages of the game instead.
• Wait, actually, more about the King: how does he work? Do you actually get to keep that 25% bonus? If so, does this let you go over the energy cap since they're not factory-produced? If I have an outpost with 100 drillers, and I own a King, and an ally sends 30 1-driller subs at that outpost, do I end up with roughly 80,000 drillers? If so, then I take back my comment about the King being awful!
• It's not clear to me why energy boosts are so good that their specialists require huge drawbacks. I got a Tycoon on the first day so I was almost always near energy capacity, but it never seemed like that big a deal: whenever I got close to my limit I'd either gift to an ally or attack an enemy. So Tinkerer and Minister of Energy never appealed to me, and I can't really imagine wanting energy enough that I'm okay with the shield/driller penalties.
• In general, I liked it when promotion required giving up an awesome-but-different specialist. Navigator -> Admiral and Smuggler -> Tycoon felt like interesting decisions, because you're losing a powerful local effect for a global (but unrelated) one. Lieutenant -> General and Inspector -> Security Chief felt less interesting, since the promoted version probably does what you want to do better than the original anyway. (I'd put Sentry -> War Hero in the latter camp too, since usually you promote the Sentry immediately after you've gotten your money's worth out of him.)
• In the interest of more specialists that promote different strategies, how about one tied to helping your allies? Half-baked idea: specialist that allows funding of players when your Neptunium is greater than or equal to theirs, and speeds up your gift subs. Except that doesn't quite work, because you can gift to yourself. (And even if you don't allow that, you can "gift" to an outpost you're about to take over.) But I feel like there's potential there, and someone smarter than me can probably make a non-broken version.