What slows down game significantly in case of multiple starts, like this one, is the detection. Basically if there are objects from two empires in a system, every five seconds the game checks if there is a detection or not. The more empires and objects in a single system, the more checks have to be done, the slower the game.
The only way to speed this up in such a situation is to use "Disable sensors in this system" option on a sensor tab in the system maps view. However, since this disables all sensors, you will be essentially blind. You won't discover jump points by observing other nations jumping and if one of the NPRs decides to attack you, you won't see incoming missiles. In fact, I'm not sure if this disable NPR sensors as well, which means it may not help you at all.
I only use this option when I'm playing multiple nations in the Sol system and I know for certain nothing will happen in the near future, so the sensors are not important. But I would not recommend turning them off when you have several computer controlled NPRs in your home system. Which means you are likely doomed to a slow game.
