I decided to try to make 3 secrecy decks meant to be played with each other. Each deck is mono-sphere and contains only 2 heroes. Of course, each also contains 3 copies of Resourceful to help make up for the limited number of heroes. There is also another disadvantage, though: we have the same number of heroes as would be present in a 2-player game, but with 3 players, so we're losing our character/action advantage from the start as well. I tried to break through this barrier as much as possible, but it's difficult. The point is to deal with things in the staging area as much as possible so they don't become a problem. Secrecy helps keep things in the staging area.
Since it's 3 decks, this is going to be REALLY long, but if anyone wants to give some feedback, feel free.
I'll explain more about each deck after each deck list.
Red Secret
Heroes - 19 Threat
Legolas
Beregond
Allies - 18
3x Eagles of the Misty Mountains
3x Vassal of the Windlord
3x Winged Guardian
3x Defender of Rammas
2x Gondorian Spearman
2x Bofur
2x Gandalf (Core)
Attachments - 20
3x Spear of the Mark
3x Great Yew Bow
2x Spear of the Citadel
3x Gondorian Shield
3x Support of the Eagles
3x Rohan Warhorse
3x Resourceful
Events - 12
3x Foe-hammer
3x Gondorian Discipline
3x Feint
3x Hands Upon the Bow
With fewer heroes to muster willpower for questing, I needed Legolas to pick up some of the slack. As for defenders, Beregond was the only choice. He has the strongest starting defense, sentinel, and his ability helps make up for slow resources a little bit. As for allies, I needed a lot of defenders (Winged Guardian, Defender of Rammas, Gondorian Spearman, and Eagles of the Misty Mountains [when built up a bit]). Plenty of enemies still tend to get through (many times it's just to get their threat out of the staging area), so more defenders is extremely useful, especially considering all of the other heroes in these 3 decks is designed for something other than defense. Some extra attackers are also quite welcome since Legolas can't do it all himself. Bofur helps us get those extremely necessary weapons and Gandalf is our only threat reduction in this deck (it's ok, you really only need to stay below 20 until you get Resourceful and the Spirit deck can help with that).
Spear of the Mark is meant for Dunhere, while Legolas gets Great Yew Bow. These two guys like to tear the staging area to shreds. Gondorian Shield is obviously for Beregond (extras can be given to Glorfindel if you end up needing to defend with him) and Spear of the Citadel is for Beregond and Gondorian Spearman. Support of the Eagles goes on Legolas, then Beregond, then another on Legolas, if you ever get that many and can afford it. This is probably the biggest issue with this deck: it's a bit expensive for only 2 heroes, even if you get Resourceful out. You pretty much need 2 Resourcefuls for this to work smoothly (which could be supplied by the other decks who stay below the secrecy threshold longer). I wish I could find a place for Horn of Gondor... I might just make it a 53-card deck and put it in there.
As for events, the choices are pretty self-evident: card draw, more defense, and more staging area attacks. Gondorian Discipline is either for Beregond when you end up getting the big baddie before you've built him up enough, or mostly for Gondorian Spearman so you can get more uses out of him.
Green Secret
Heroes - 12 Threat
Mirlonde
Pippin (The Black Riders)
Allies - 20
2x Haldir of Lorien
3x Ithilien Tracker
2x Ithilien Archer
2x Henamarth Riversong
3x Master of the Forge
3x Gleowine
3x Warden of Healing
2x Gandalf (Core)
Attachments - 15
3x Asfaloth
3x Elf-stone
3x Ithilien Pit
3x Ranger Spikes
3x Resourceful
Events - 15
3x Secret Paths
3x Daeron's Runes
3x Deep Knowledge
3x Out of the Wild
3x Risk Some Light
I chose Mirlonde and Pippin because it's the lowest amount of starting threat you can muster with 2 heroes in Lore (or any sphere with the exception of Glorfindel + Spirit Pippin). They also both have 2 willpower, which is pretty good for such low threat and for Lore. Grima might be a good choice to swap with Pippin, if you can keep his ability from causing your threat to get too high, because his ability helps cover for the lack of resources.
The rest of the deck takes a bit of Ranger theme. We're trying to control threats, so we use rangers, traps, and encounter manipulation. The traps work well because Ranger Spikes can allow Legolas and Dunhere to keep beating on big guys while they are stuck up there, and Ithilien Pit works well if you have enough attackers laying around to take guys out without them needing to come down and make you use a defender (if their engagement is low enough).
We've got Haldir and Ithilien Archer to provide some decent stats while Ithilien Tracker proves to be amazing when you don't have any Ranger Spikes sitting around (or enough resources to use it). Master of the Forge and Gleowine obviously help us to get through our decks, and specifically get the traps out early. Henamarth is there for a tiny bit of scrying for when you don't have any of the events handy, though his impact is quite limited in 3-player. And we have Warden of Healing and Gandalf for obvious reasons. Warden of Healing becomes extremely handy when the Red deck can't get enough defenders out to soak up the damage for the other decks.
Asfaloth is an obvious choice when Glorfindel and a Lore player are around. Elf-stone helps the decks get Gandalf or other powerful, but expensive allies into play. And you already know about the traps and Resourceful.
The events are all about card draw and encounter control. Secret Paths is the one way that we can really deal with locations, while most of the Ranger-themed cards are more for enemies. Out of the Wild and Risk Some Light are amazingly powerful encounter control cards, especially in secrecy where they only cost 1 and 0, respectively. Deep Knowledge shouldn't be a big issue with decks having this low of starting threat and it helps everyone with card draw, which is invaluable.
Blue Secret
Heroes - 13 Threat
Glorfindel (Foundations of Stone)
Dunhere
Allies - 20
2x Arwen Undomiel
2x Bofur
3x Ethir Swordsman
2x Northern Tracker
3x West Road Traveller
3x Westfold Horse-Breaker
3x Escort from Edoras
2x Gandalf (Core)
Attachments - 15
3x Light of Valinor
3x Ancient Mathom
3x Unexpected Courage
3x Leaf Brooch (proxy)
3x Resourceful
Events - 15
3x The Galadhrim's Greeting
3x Elrond's Counsel
3x A Test of Will
3x Hasty Stroke
3x Dwarven Tomb
Glorfindel is an obvious choice for secrecy decks, and not just because of his low threat. With Light of Valinor he can also contribute attacking or defending without needing to waste an Unexpected Courage on him. Also, with Asfaloth, he becomes possibly overpowered. Dunhere works well with the theme of dealing with things in the staging area, and with the Spears of the Mark from the Red deck, he can wield an amazing 7 attack.
Arwen is there for obvious reasons, not the least of which is giving Defender of Rammas the sentinel keyword, or giving Glorfindel a more respectable defensive strength (his one weakness). Bofur gives us the choice to save a resource for A Test of Will, but then pop in more willpower if nothing evil shows up, and if you do it when he won't be enough to get you to quest successfully, you get to keep him there. Ethir Swordsman and West Road Traveller are mostly there for more questing power, as is obviously true with Escort from Edoras. Northern Tracker supplements Asfaloth and Legolas to clear locations more quickly, while Westfold Horse-Breaker offers a tiny bit of willpower while we wait for a chance to ready a hero in need.
Light of Valinor is obvious, especially in decks like these where more actions from our heroes is invaluable. Ancient Mathom rounds out our card draw. Unexpected Courage is an absolute must. Steed of the Mark is pointless because the two heroes than can hold it don't quest and we can't waste resources for it anyway. Leaf Brooch works best in this deck since it has the most expensive events and of course we need more resources. If you end up getting multiple, you can pass one to another deck. Red will likely no longer be under the secrecy threshold, and most of Red's and Green's events are free, but you can probably get a couple good uses out of it. Otherwise you can place another on one of the blue heroes in preparation for Galadhrim's Greeting.
Galadhrim's Greeting and Elrond's Counsel are obvious threat reduction cards. A Test of Will and Hasty Stroke are pretty necessary when you have many weak characters and losing any one of them is a bigger loss than usual. Dwarven Tomb allows us to reuse any one of these amazing events, most often A Test of Will.