How different and difficult is 100% ,200% and 500% percent difficulty?
Like enemy ship size, their economy and thing like that, will they spam behemoth ships or just small ones but there are thousands
No, it just means how much the NPR will be scaled in comparison to the first player race. There is also a random element but basically 100% means that on average NPRs will spawn roughly equal to the player but sometimes they might be bigger or smaller. If you put in 200%, then on average the NPRs should spawn twice as big as the player and the odds of an NPR being equal to you or even smaller are diminished.
Note that bigger here does not mean physical size, just that they have more research points to use, more ships to begin with, and more population on their colonies, that sort of thing.
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Is there any way to force them to use bigger ships?
No. NPRs use their own templates made by Steve and they would not even understand how to use a ship designed by a player even if you edited the DB and gave it to them.
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For game-start NPRs, if you use the Customize NPRs option you can manually set the approximate relative size of their ships.
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I wish you could change them in game
Pity