The problem is it doesn't represent the overwhelming portion of history. Scientific advancement came from places that had a head start in settling and could build an organized society and it came from competition and trade (while I don't think "tech trading" is realistic and I suppose research agreements are OK, I would also have liked techs researched by other civs to be cheaper). I'm trying to think of when government investment to promote science first became important. For military, I'd say the second half of the 19th century. For non-militaristic achievements, I can only think of things like the space race.
Neither system is ideal. The current version still rewards gold investment through research agreements and whatever that social policy is that gives you beakers on trading posts (I suppose that represents science through trade, but that might be a stretch). If you want gameplay mirroring reality explanations for why Germany should have a higher science in game, it's because they have more scientific buildings and trading posts and have completed far more research agreements than Nigeria. It's also because Nigeria was conquered for part of the game and is only now an independent civ once again.
There are examples of leaders donating to the church in exchange for the establishment of monasteries as far back as the middle ages, and this was at a time where research was done predominantly in monasteries and mainly benefitted the local nation (although it spread somewhat by church communications). Beyond major projects, how much technology is developed in a nation these days is largely a matter of the research spending of its government. Programs to attract top professors and provide them with good research facilities and spending (grants) are a huge factor in technological development.