AI Spying Problem

Unused spy points go to defense. You need more intel centers generating points.

Defense points also get "saved up". I don't know the particulars, but it can be difficult to start spy operations against an empire with a large stockpile of defense, even if you have much more intel than they do.

Can't help with your second question.

well, u could create ur own system by playing with all teck and only neutral enemy... then u change the world u are in as u like, u save the map and play a new game on the map.
To start in the system u want, when u start a game only put 1 place u want the player to start in, u will be a that place because u are the first to be place in the game.
Well, that is how i'm use to do that but its been months since i played so i'm not really sure...
good luck and try that

in your Space Empires folder there is a folder called Utilities that has a program called MapCompiler and a couple of text files.

I haven't used it myself and I believe it was added in one of the patches but I have it with patch level 1.44

You can also set your game options to disable intelligence all together, so no one can spy or sabotage.

It is useful to note that a new empire doesn't start on a planet of an existing map. It's easier to just spawn an entirely new planet (in the chosen starting location systems).

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Playing Touhou games (Go here if interested . No, nobody else is that good/insane as that replay). No rush for SE V bug fixing.