While it's always nice to see an expanding, living universe, there can, especially in long slow games, be a serious issue with bloat that the player will never see, and so adds little or nothing to their game.
An option to cap the maximum number of NPRs(you can just set NPR generation chance to zero, but unless you start with that and set the starting NPR count to the desired max total, you can't set the max number that can be in the game, and starting with multipule NPRs invites other slowdown issues), and/or an option to stop NPR exploration - or atleast prevent them from going through jump points that would generate new systems more than 1-3 jumps from home, so you still get pocket empires - would be a nice way to give players a way to mitigate that concern and prevent games from being brought to an unexpected end by AI curiousity.
An option to limit NPR generation to pre-TN civilizations might be nice, too. Especially for RPing. Give players more control over the scenario they want to play.