AFAIK, the espionage system hasn't changed much (if at all) since DA. It takes longer to train a spy now, because it is more difficult to generate the BC.
The AI has been taught how to use it's spies more efficiently. Not that many players paid attention to this part of the game, but evidently, Frogboy did.
I'm already finding that I need to start building spies early in the game to counter the eventual espionage attacks.
Good advice. It is advisable to build up a stock of spies as the funds become available.
You only need to be concerned about defending against the AI spies if you find yourself in a period of protracted peace. In this situation, the AI can get very passive/aggressive. If you can manipulate it into open war, then the spies will go away- the AI is much more concerned with building warships.