Maybe you can treat the corporations as characters with various skills like (Mining, Refining, Construction, Farming, Food Processing, etc.) and you could see this on their "character sheet". Corps with higher skill levels will be able to develop related industries faster, and more efficiently. These skills would level up over time as they develop industries related to those skills. The final yield of whatever is produced would be modified by your government's technology level plus whatever related patents the corporation has.
Yeah. Uniqueness/specialization of corporations is sweet.
I'm also thinking of simplifying the planets and making corporations more complex. Like no industries on planets, just generic factories. Then the Emperor (the player) grants a charter (monopoly) for a planet to one corporation. That corporation can use the assets on the planet (factories + resources).
You don't produce anything on planets (OK, almost anything :D), but instead produce "on corporations". So you have like 5 companies and 5 production queues.
To produce something (like ships) you need ONLY money (you sign a contract with a corporation to deliver it). But, the corporation require resourses, labour, etc and if they lack it they might ask for more money, do it slower or even fail to deliver in the worst case scenario. So, you care the most for the money, but also you care for your corporations because if they prosper you can get goodies from them cheaper and more reliably.
Corporation would have "technologies" or "assets", like if some have electronics factory and a shipyard they can produce space ships. I suppose there should be some way to influence how the corporations specialize.
Now, if the gameplay is too simple (I need to increase food during food shortages, I need to increase tech to improve my building capabilities, and I must spend everything else in research 'cause otherwise I'll lose), that could be boring.
You know, I like the food less and less. It's... I don't know, not so great.
Maybe like this: you need to care about food on strategic level only (how many fertile planets there are in the empire) and you have some single slider saying if you subsidy the food production and how much (also research in agriculture can boost it too). Then there is "food price" variable which is the amount of food you have in the empire / by population. It affects the population growth (cheaper food = more population).
Another way to look at it is to specify a project from a tech tree. Instead of spending research points on research, etc. you could just buy it outright.
Research is yet another topic. I would disconnect it from economy (planets do not produce research points), instead some sort of Paradox style "base research + literacy + investments in education" would determine how much research you have (a great side effect is the research would not snowball at some point when you have tons of planets).