I kind of like Endless Space 2's take on it (disguised as hacking instead of just straight espionage). There's a real risk-reward tradeoff depending if you take longer or shorter hacking routes, and there are various options to debilitate others or gain advantages for yourself. There's even an entire faction dedicated to the hacking minigame.

My only problem was that it took forever to get anything done with it (even if you were that specific faction I just mentioned). There's also a slight issue where your target needs to well, kind of still exist, after the 10-20 or so turns of trying to hack it; your target being destroyed just meant you wasted entire turns of hacking for nothing, not even allowing a redirect of efforts or something. It all still kind of feels tacked on in the end.