I make very little use of agents, especially since I tend to play like a gorging behemoth and go military expansion style like crazy. And I find managing scores of different agents to get immensely tedious with a big empire. I use emissaries, obviously, and sometimes a dozen spies to try and stir up an enemy province, but I find assassins to be very time consuming to "train up" and immensely vulnerable. Inquisitors are way overpowered, especially the Grand's, because all the time put in valouring them up is pretty much safe since Inqs don't suffer from death-by-botched-attempt. I will happily and without any moral pangs pump out a bunch of them to annihilate my most annoying enemy's cream. But spies and assassins, barely make use of them. Even emissaries tend to get left out later in the game since no one wants to be allied with me anymore anyway.