at the start of the game, use SM race (not the player race) to generate systems. Delete ones you don't like. When you get one you like, start an NPR in it and set its minerals really high, like high enough to never run out. Do this for a few systems and turn off NPR discovery chances. You won't know when or where you will encounter these NPRs, and as long as you didn't do the generation on the player race you won't have the systems pre-ID'd. Without NPR discovery chances they can't roam the universe and slow the game down by generating NPRs that are meaningless to you.
The high minerals are to stop the #1 killer of NPRs: Mineral crunches. Mineral crunches kill player starts all too easily, and NPRs don't get the benefit of starting in the rich Sol system. Give them high minerals so they never get stuck. If you invade and take over an NPR homeworld, set its minerals back down accordingly.
You could also set up one of the NPRs as the Big Bad Granddaddy, with at least a couple tech levels on everyone else.