Well if you play the blitzing game then you might find spies and assassins less useful. Though playing in this way also leaves you very vulnerable to the bloat effect, later on and poor territorial stability in general.
As to tedious management, I disagree somewhat. Spies require very little management. As I've said before, you leave them in the province and let them do their job, it's only when you start having problems with a rival faction's rogue assassin that you need to move your best spy into the problem province. Assassins require more work and care. Because they follow targets they tend to get trapped by border forts a lot. So it's important to cancel the mission if the target moves and forget about sending them into border fort provinces unless they're about 5 star and the mission is really worth the risk.
Inquisitors and especially Grand Inquisitors are an horrendous exploit. I used to have a rule of 1 Grand Inquisitor and 3 Inquisitors only. Nowadays I don't train them at all.
Emissaries are my least used agent. I prefer to use Religious agents for diplomacy. I only keep an Emissary for bribing and stripping titles and that's it. Emissaries are also very big targets for rival assassins. The AI seems to be tuned up to go for those first in preference to any other agent or generals. If you want to train your spies up keep an emissary in the province as bait.

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