Agents\Heroes can be fun in Total War, but as the difficult level gets higher and the AI gets more extreme bonuses and everyone starts to solely target you it can hit a critical mass where it becomes way more annoying than enjoyable. So what else is new with Total War and how they try to make the AI a challenge at higher difficulty levels.
Agents in Empire, Napoleon and Shogun II weren’t really as massive an annoyance to me since while they could be powerful I rarely found them running around in the same numbers that the AI spams them in Rome II and later titles. Whether it was because there was actually less of them in play at the time or the AI just wasn’t as single-mindedly hell bent on making your life miserable with agents, Shogun 2’s agents are largely this style of agent done right to me.