Hi. I liked the Spy system in EL, at least more than the hacking system in ES2, but I think it needed some improvements and I imagine it is probably going to end up as one of the first DLCs for the game.

The Good part of the system:

It was fairly intuitive. You want some guy to "spy" on your enemy? You send your forces close to one of their cities and then your Spy "enters" it and then you wait for a while for them to infiltrate the city so they can perform an action. You want to increase security in a city, you start controls of a vague sort to make sure it is secure, even if it means slowing things down.

It allowed players to interact with enemy empires in unique ways, such as highjacking their view, stealing their Dust or copying their Technologies.

The Bad part of the system:

It was a bit too heavy on Micro and waiting, so it could very easily be forgotten and neglected.

Investing on researching and building Security buildings felt bad because they didnt get you close to victory in a meaningful way and you couldn't quite tell if you were being spied upon against a good opponent until it was too late.

Performing Crackdowns was similarly annoying since you lost production and since the results of the Spies were partly random but the loss of time performing them was guaranteed, you often felt like just not caring and hoping the Spies failed was the best idea.

Not a big problem, but I also felt like it was tied a bit too heavily to only Forgotten when other factions like the Cult, the Roving Clans, the Morgawr, and the Mykara would have made sense having some unique interactions with the mechanics.

What to do then? I think increasing Security should have more natural ways to be implemented into the game. 

How?

I say fleshing out the Governor mechanic would be the best idea. Governors are already a cool and popular concept, so giving each Governor their own screen in the cities could be well received. Governors were already a prime target for Spies in their mechanics so the natural enemity would be played up. You could go to your City menu and check for Governors and find a list of Governors you have and you can scroll through them. 

And what could you do with the Governors to control Security? You could naturally tell Governors to focus on a particular area of the city, be it:

1. Military
2. Population
3. Economy
4. Government

And you have each of these areas have their own Security Level in a scale of 0-10. The Security Level could be naturally a 3 at 100% Approval, and go up to 10+, with a Governor focusing on a particular area of government granting it a Security of +5, so 8 without any improvements, just the Governor focusing on that one area of the city makes it mostly safe and resistant to spies.  I feel like most Espionage Actions could be easily divided so they'd mostly affect these areas.

And outside of the Security/Espionage mechanic you also get a small buff to the production in that area of say 10-20% while the Governor is focusing on it. You could maybe make it a bit more complex introducing some kind of experience, ideology and/or relationship mechanic with each Governor, but it is not necessary.

I think this would "feel" better because you'd be able to increase safety against some Espionage actions without spending Research and Industry on it.

And there would still be Technologies and Buildings that increase Safety or give Spies extra options, but they'd come in packaged with other stuff that also increases production in that area, even if just a little.

And what to do with Spies?

I think they were mostly fine, although I'd make a change: Let players put multiple spies in a City which would make Infiltration go a little faster, make an action that allows Spies to make it so other Spies can Infiltrate faster and make it so you need multiple spies in an Empire to perform some of the most powerful Spy actions like taking an enemies' vision.

Also, after you capture a Spy or Governor, you can Sell them to the Market instead of keeping them prisoner. Even Event Heroes. And players would have to repurchase that Event Hero after a few days to continue their Quests related to them. I think this could make the rewards of capturing high level Spies and Governors a bit sweeter.

And what about Stealth?

Personally, I feel like it was a bit broken in EL and it made it almost impossible to grant to other factions at a reasonable price. How to fix it? Keep Stealth very rare,  but make new Capacities that grant new versions of the mechanic. In particular:

Sneaky: Makes units invisible AS LONG as they haven't performed an action this turn.

Forest Camouflage: Makes units invisible in Forest tiles.

Sand Camouflage: Makes units invisible in Desert tiles.

Snow Camouflage: Makes units invisible in Cold tiles.

I think these capacities could be distributed more fairly accross Minor Faction units and some major faction units that could deserve them even outside a "Stealth-focused faction".