try using the probe ability on tec scouts

Isn't spying already kind of done? You have scouts for one thing. The TEC scout, as said earlier has the probe ability. The Advent one has Lingering Presence. They also have a capital ship (Revelation class?) that has an ability to veiw other gravity wells for a time, they can see the spread of culture anywhere, and they can see any planet under the influence of their culture. The Vasari can see all ships in phase space.

Bring my beloved Haegemonia back to the table.

Spies were invisible unless detected in this and they had multiple abilities which increased as their rank increased:

The Spies would have to float in position and would have a chance of the mission you give them succeeding depending upon their level and toughness of the mission

Steal Money

Get Planet Information

Get System (Grav Well) Information

Get Empire Information (See the state of their money etc.)

Sabotage Ship (used to take out star bases)

Detect Spy (you'd have a few spies dedicated to detecting enemy spies in your systems)

Assassinate (equivalent in Sins of resetting a Level 5 Ship or whatever back to Level 1)

Incite Revolution (Explains itself)

Get Intel (This was always my favourite. You can steal a single item, has to be first on tree, from an enemies research tree although this may already be research you have or the equivalent. You could however get for your army a valuable piece of enemy research.)

I think spying could work well