1/ More story campaigns
2/ Improve battle mechanics, so it's less mechanical. And also make researching/using defences economically more viable.
3/ Economy revamp. This involves de-linking tax revenue from population to some degree. Perhaps multiple tax rates a la Sim City, with appropriate impacts. Trade should be overhauled significantly so that initiators of trade get money, not buyers of goods (balance of payments - basic economics). Buyers actually to pay the money. But buyers get some social benefits, primarily morale. Value of trade to be linked to distance as now, but only perhaps 30% so, the other 70% of valu to be determined by a new factor that you have to R&D i.e. trade goods quality.