Slitherine

Redid the mod real quick without anything else.

Installing instructions (stolen from Blackarchon's mod):

Download and extract this file to the following path: "C:\Users\<your_username>\AppData\Roaming\Proxy Studios\Pandora Beta" (or "C:\Users\<your_username>\AppData\Roaming\Proxy Studios\Pandora" if you aren't using Pandora Beta)
Note: You won't be able to see this folder with the Windows default settings - you have to enable "show hidden files" before.
Pro tip: Hit <Windows>+R on your keyboard, then enter "%appdata%" - this will get you faster to "C:\Users\<your_username>\AppData\Roaming\"!

The simple solution to cheap wins is just to not use them--I just don't use spies, but don't mind defending against them.

What would be great is to make them more balanced. Maybe allow defensive spies in cities, and offensive spies have to defeat before they can conduct their missions, or at least have them make missions more difficult. Or just reduce the effect of spies, especially in small cities. Of course I'm sure that would take code changes, including AI code to have it actually keep spies in cities to defend.

A rework of spies is considered.
I think a first big step in the right direction would be to scale the amount stolen with the size of the city that is spied from in relation to the total population of an empire.

Having that newly founded nearby colony give you access to steal about 100% of their research and credits every turn is just ridiculous. Citysize/TotalPopulation of their research and credits would be much saner.

Is this useable if you aren't using the 1.5.5 Beta? (I'm going to try anyway, but thought I'd ask)

Yes, sure.

This mod is incompatible with 1.6.0 and, in my opinion, also no longer needed since the spies have been toned down enough to not feel as brokenly imbalanced as they did before.