I found as I ran intrigue games that at a certain point mechanical and plot actually go hand in hand. Encounter design is about providing obstacles for the party to overcome. Social interaction is no different except in the nature of the obstacle. Instead of we need to cross the bridge and it is guarded by 10 orcs now you're talking about we need to speak to the duke and he's guarded by four layers of toadies and protocol. Or we need to consult Divination for Dummies but the only copy is kept under glass in the University library, or whatever. You gates and obstacles, and motivation for the PCs to overcome those obstacles.
So, make it personal: kidnap a friend, infect an ally or party member with a dread disease, frame the PCs for crime they didn't commit, use countdowns to 'BAD THINGS'. In a mystery/intrigue game the PCs need information, so gate that information behind obstacles and make sure there's not too much doubt or ambiguity involved. If you try to get too cryptic and fancy you risk the players not being able to connect the dots.
