So 80 years into a conventional game and I've gone from losing 300k tons of ships 40 years ago against the alien menace to destroying a million tons without taking any losses and only a few armor hits (this is on 200 percent difficulty).
Turns out when we first met 40 years ago they had at least 1 level of tech on engines on me but now 40 years later I out tech them in many fields.
I finally finished a new fleet with full training and sent it into their home system and went around blowing up ships wherever I could find them and found numerous alien colonies spread around the system. I pretty much have space superiority, what should I do now? The ground combat is kinda painful to do right now especially with all the bugs. Should I bomb them to the stone age?
What do you do when you have full power over an NPR? Before anyone says peace I am already at peace and trading with another NPR.
There are many things you can do to make sure you don't move past the NPR in technology and power too fast.
You can play a conventional game with slower technology... it will take allot more time to catch up.
You can put rules and regulations for both industry and research mechanics so you can't "optimize".
A few examples...
1. I only allow labs to be provided into ONE research category and I can't switch them to another category unless I'm willing to transfer two and SM out one of them from the game. That forces me to spread out the research which is much less efficient. The government usually require several things to be researched at the same time as well (even if that is very inefficient), that is what governments do.
2. Use industry in a more realistic way... you can't just switch industry from one project to the next in reality.. make sure you only can change industry by about 10% per year without any penalties. If you want to switch more you need to put part of the industry on hold... I generally only allow about 10% change per year anything above that I only get half and then every year I don't switch more than 10% if get half of it back or all if it is 10% or less and that is all that I switch.
Both of these options will force you to make more realistic long term choices.
Another way is to role-play a bit more. Sometimes people are not wanting what is efficient but what they feel is more appropriate to them not the community. Allow your administrators traits to govern how they develop colonies even if it is not optimal.
People generally don't live for making the government rich and prosperous and individual leaders might have different ideas what is the best use of resources. A colony might want to invest whatever resources they make into their own colony rather than support some foolish venture into the other side of the galaxy. They might rise up against the huge expenditure of the military ships and ground forces instead of developing their colonies and transform a new planet which is a potential colony... etc...
Don't play the game from YOUR perspective but from the perspective of the people living in it, try to find out what it is they want and make sure that different leaders, parties or whatever governing structure you have strive for different goals and agendas. This also means they make decisions from what they know works and don't work, they have no idea how the game mechanics work or have any previous experiences from past games. Most societies no matter how structured or empire like they might be will have to deal with people as individuals at some level.
In short... there are MANY tools of which you can play the game so NPR still feel like a challenge over the course of an entire game.
In my opinion the NPR are just in the game for you to experience some conflict and challenge you. Playing the game is the ultimate goal and "winning" the game is not what it is about. Therefore it is better to find some interesting role-play aspect that you like and go with it... the more restriction you put on yourself or the more problems you give yourself the more you will feel satisfied when you do well in the end.