[Urendi Maleldil]

You could mod a new advanced racial trait to give planetary cloaking facilities, cloaked ships, and special intel projects. You'd need to leave some planets uncloaked because you need diplomatic contact with a race in order to perform intel against it (poor design, but we can't change it).

You could then mod the AI so it will build fewer colony ships or none at all. If you're using intel, then you'll probably want to leave lesser colonies (like mining colonies) uncloaked so you can intel your neighbors. Just add AI facility construction calls for cloaking facilities to all colony types except those.