Technology and research in the strategy genre has become stale. Games today use the same system that they have used for years. A TBS like this would generally use something like the civilization system. You choose a research goal and then your people funnel all their creative energies into a nicely packeted 'technology' that then has an instant beneficial effect all across your empire. I'm sick of it, and I see many other peope are too. That system may be slightly realistic and somewhat interesting for a post industrial era society but it is completely out of place in a medieval setting. I say we scrap that system entirely and create a new one from scratch. Something much more organic and also something more intuitive that would require less micromanagement. Let's start off by borrowing a few prinicples from reality.
1. Ideas are nearly impossible to contain. Ideas like horseback riding cannot be kept from your neighbors. Once they see you riding horses and using them effectively in battle it is not going to take their sages long to come up with the idea also. Heck the footsoldier on the battlefield facing a calvaly charge probably came up with the idea in the first five minutes of seeing those horsemen. Also you see someone irrigating. How long do you really need to contemplate the concept before you put it into practice yourself a farmer would instantly see the value of it.
2. Revolutionary ideas like horseback riding or irrigation do not come from scientists. They come from bright people in field who see a problem and come up with a solution. I bet I know who came up with irrigation... I bet it was a farmer. There are things that could be done to encourage ideas. Things like education, experience, social values etc.
3. Education is more important. Just because your society knows about irrigation doesn't mean they can use it effectively if your people are all ignorant.
4. Implementation is more important than the idea and comes in stages not all at once. Ok. You saw them riding horses. Yes you can now go out find some horses and put riders on them. That doesn't mean your riders will be as effective as their riders. They may have had decades of horse breeding programs. Their riders may be trained from birth to know how to handle horses. They may have spent year perfecting methods of teaching their war mounts not to spook in battle. Their tacticians may have knowledge of the intricacies of formations that your people have never heard of. You both have cavalry but theirs are infinitely better.
So how can this really be applied to a game without making it ridiculously complicated? I think there are many ways of doing it but here's mine that may work and create something new and interesting.
Ideas are generate by your people automatically based on their education/knowledge/experience level (this would be a city level statistic and would be in several categories). This level can be increased by building educational buildings, spending money to support bards, teachers, and scholars, and by having and using 'ideas'. The different levels would change depending on what most of the people in that city were doing. A city that focused almost exclusively on farming might develop good techniques associated with that but probably would never have an idea associated with architecture. Ideas then automatically spread to other cities in your empire and cities of neighboring empires depending on the spread rate of that idea and the education level of the cities (some ideas are extremely obvious once seen and others are more suble, also educated free thinking cities would pick up on an idea much faster than a backwater farming village). You could of course try to inhibit the spread of an idea to other empires or pay to have it spread across your empire. Also some ideas would only come from cities that had high knowledge levels in multiple fields making it beneficial to focus on having a few large cosmopolitan highly educated cities then a bunch of faceless towns.
Cities with high knowledge/education/experience in certain areas would be more effective in doing some things and couldn't be retooled easily. You can't just instantly turn a farming village into a mining village and expect it to perform effectively. In this way I think we would have a much more interesting research dynamic but also it would help to give cities character. Cities would in a sense be like RPG caracters with stats that could be leveled up.
Edit: I'd like to add to this also. There still would be 'research'. But it would only be done by your sovereign and maybe heroes and would be all about research into magical schools and also maybe more mundane 'secret knowledge' something like some mystical martial arts style, deciphering the language of the dragons, how to make napalm, or discovering how to use a pre cataclysm artifact. Things that would be possible to hide but would require dedicated scholarly research and experimentation to be effective. Although many of those might only be possibly to research if the proper idea had already been generated and your people knew of it.
Also this would take away from the 'technology is king' paradigm. Because you could not totally outstrip your neighbors in technology so that you were in a totally different era of technology. And also a peaceful research focused empire would not have superior military 'technology' to a organized military empire. I think it would really give character not only to cities but to empires.