That has to be the most frustrating part of the game for me. Once you "figure" out how to play the game, it can be tough to find NPRs or other spoilers that actually give you a challenge. I had a game in the VB version that was super crazy fun because Sol got invaded and I was fighting tooth and nail. Ended up losing, but to this day, it was one of the funnest games I ever played. I think if I had done better and "won" that fight, I doubt I would have had any challenges past that one NPR based on my experience in other plays.
In anycase, if I remember correctly, the difficulty modifier will increase NPRs research speeds. They aren't very good at optimizing research labs and that's why they fall behind. Another thing some people do is limit the number of labs they employ.