Take merchants, for instance. Guide them to an ingot of silver, bolt of silk or similar resource then leave them there and they send back a trickle of florins to your treasury. On occasions wheeler-dealers get bullied off their pitches by more experienced AI competitors. This low-key economic warfare is a risky business. Success aggravates foreign powers and failure can result in the aggressor closing up shop permanently.
Spies and assassins have been a crucial part of the Total War experience ever since the series started and they are as important as ever in Med II. Hooded hitmen scamper everywhere for a few turns, hitting each other, then getting hit in return. It's splendid to watch, especially when your top operative emerges alive and kicking with massively enhanced stats.
Adding to the pleasure of covert capers are amusing pre-rendered cutscenes illustrating the mission results. Cannily, success and failure sequences start the same way, so you aren't instantly alerted to the result the second the clip starts.
Above: It looks amazing, but street-fighting can still be fiddly
Remember the inquisitors from M:TW? They are back with a vengeance (and a big sack of blood-caked interrogation instruments) but are only available to the Papal States. If you treat religion as dismissively in Med II as you did in M:TW you'll rapidly come unstuck.
Let things slide and eventually, in addition to visits from the holy arsonists with the thumbscrews, you'll face Rome's ultimate sanction - excommunication. Other states look on excommunicated nations as strategic sweetmeats. If things get really bad you might even find the Pope's decided to give Jerusalem a year off and sent a Crusade in your direction.