Start with what you know can be modded in SE4, and then sprinkle on a bunch of ideas that would be cool, but may or may not be possible.
It is not unreasonable to begin planning out a universe for your mod to exist in, though. You can worry about implementation and which things can or can't be modded later.
Decide on the ideas and balancing factors behind your weapon classes, defenses and economics,
galaxy layouts and so on.
Once SE5 arrives in your mailbox, then you merely have to implement all those ideas, and you can be fairly confident it will all work together and be balanced.
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That's my theory anyways.
