The first 100% bonus on research, manufacturing, or economy should be 100%. For example, 3 factories with the correct adjacency bonuses should provide 100% bonus to production.
However, if you build a 4th factory on the planet, instead of providing a 25% to manufacturing, the 4th factory will only increase manufacturing by 12.5%. In other words, each factory past the 3rd one is half as effective as the first three factories.
Once you get a base manufacturing bonus of +200%, each further factory is only a quarter as effective as before, and so on and so forth.
This would discourage uber specialization of planets and the sort of idiocy we see where a planet can produce +500,000 credits per planet. It would also make the AI better because the AI really sucks at uber specialization.
Also, factories past a certain point should produce pollution on a planet, decreasing its approval and pop cap. Synthetic races, however, are immune to this.