I know espionage as it exists gets a lot of gripes and a lot of players don't use it. Personally, I'm a fan, and have had a huge amount of fun and experience using it. Like others, I agree it needs some work, but the system itself isn't a complete throw-out. I'll provide some more detail, below, but be warned, this will be a long post.
Current Use Cases
- Tech draw manipulation
The strongest current use case for espionage is to facilitate rushing particular techs. Due to the way that advancing tech levels draws more cards into the pool of potential techs, high research empires currently shoot themselves in the foot when tech-rushing, as they increase their draw pool even as they draw towards their desired tech. Steal technology requires a little time and thought investment and the payoff is one or two tech cards that are revealed mostly researched, but incomplete. Most importantly, this adds the card as an extra research option and removes it from the draw, allowing the player much more control over what tech tiers will be in the next draw.
Pros/cons: This use case helps us to take the edge off the sometimes very annoying randomness to the tech, and mirrors real world actors. This showcases, for me, how espionage should be working across the board.
- Scouting
Currently, the only way to scout opponent's closed borders in the early game is through espionage. This puts a reasonable and realistic limiter on players who want to bum-rush an early neighbor, and helps to maintain some mystery in the galaxy for late game. Particularly strong is the fact that your knowledge of an empire's key facts can be stagnant if you have scouted them previously, which interacts interestingly with their encryption level. In the early game, this is much more impactful, as having no data on a system prevents your combat ships from jumping in, which promotes thoughtful gameplay. In the late game, the same mechanic allows us to see, and therefore counter, our opponents' ship layouts.
Pros/cons: For the most fundamental use of espionage, this is one that I find doesn't impact the game enough. The issues are that the benefits land at super early game or unreasonably high levels of espionage (ship layouts). Scouting before conflict is definitely something the player should have to do, but the first tier of sensors alleviates the hard lock against players jumping into systems, and most players will send a doom-stack of many fleets, so strategic positioning and knowledge of enemy movements is not something that Stellaris does. Universally good weapons, like disruptor spam further draw away from the intended specialism vs counter style in combat.
- Political Manipulation
Influencing other empires is another current usage scenario, but doesn't see a very strong practical impact, currently, due the randomness of the action and how empires currently block together and form unassailable friendships.
Desired Use Cases
- Better Political Manipulation
Greater influence over the political game is the main need for espionage in the future. Formation of unassailable federations or vassal clusters shrinks down diversity in the galaxy from the late early game and draws up permanent political borders, which cannot be crossed outside of war. The favour system, whilst unbalanced due to lack of AI interaction with the system, was a starting point which allowed us to tweak the decision-making for other factions in a meaningful and sometimes very powerful way. Previously, using espionage to obtain favours was valuable, and a similar mechanic in the future, that the AI can also use, will become impactful.
Similarly, more capability to sour or improve relationships between empires of our choice would be impactful. However, all of these capabilities need to also be something the AI can engage with, else the player will not be challenged.
- Useful Sabotage
More impactful sabotage is needed, to encourage espionage usage around war and military disruption. Currently, AIs have to cheat to a ridiculous extent and planting a pirate camp in a trade empire will have no noticeable impact on their ability to generate ships or fight wards. I have no idea if AI factions patrol trade routes, but most of the time, AI's will generate their own pirates and comfortably ignore them, so for the most difficult Operation, generating piracy feels particularly worthless. Sabotaging a star-base is a good one, but the fact that you only damage one module and can only undertake one operation at a time prevents this from being useful, as you will still need a massive fleet.
A peripheral change, allowing conquering factions to build, restructure or enhance captured star-bases during a war would make sabotage more viable, if it were also able to affect more modules. For example, a weaker empire with strong espionage could sabotage a fortress star-base on the border in order to win a difficult batter, and then could repair or enhance the star-base and could use that to bunker down, preventing re-capture. This kind of strategic interplay is what we should be seeing.
- Theft
Resource diversion is not something that espionage does at the moment, which leaves highly spy-focused factions at the wrong end of opportunity cost. A way to use espionage to offset the weaker economy, by allowing the stealing of resources, is necessary to enable factions to offset not making economically sound tech, tradition and influence investments. Currently, spying costs influence, which makes sense. Spies being able to steal influence if their operation is successful would make espionage more niche, in that subtle and spying empires become more 'influential'. However, basic resource theft is appealing.
Other Changes
- Influence cost
Currently, influence is the most carefully guarded resource in the game. Even the most profitable use of spying currently is in direct competition with establishing a new star-base, and the more diplomatic an empire is, the less they can afford to spy. This fits the Romulan Star Empire, but is antithetical to how real world politics and espionage interact.
- Envoys
Whilst it has some thematic place, the choice between diplomacy or espionage is currently deepened by the dual use of Envoys, who are too rare to split between the two. As an alternative, instead of allocating an envoy to diplomacy and one to a spy network, we could use the same envoy - i.e. an envoy harming or improving relations also enables a spy network to form. This makes real world sense, as it requires engagement in the local political system to insert spies.
Making Envoys into a proper leader type, with its own cap, could also add fun ways to improve espionage involvement, through use of leader traits.
- Frequency/multiple operations
Currently, we are limited as to how many and how frequent our operations are against a specific empire. This can make sense in the case of steal technology, gain intel and acquire asset, but prevents operations that affect faction relationships or have a military impact from being useful. An empire that can afford it should be able to spark piracy across multiple zones in an empire, sabotage multiple star-bases, or attack a faction's reputation on multiple fronts.
TLDR
The system as is has promise, and already has more use than players give it credit for, but to improve its relevancy, the costs need to be more manageable, the outcomes stronger and playing without engaging with the system needs to have more drawbacks in terms of intel.