Why has the IO-390 not replaced the IO-360?
Short answer: OEMs don't see a big enough return on investment (ROI) to justify the change.  

Long answer:  Getting an STC is not a simple or cheap process. It costs a lot of money. The recovery off that cost has to be factored into the sales price of the updated aircraft. And there are additional costs associated with supporting a new model of an aircraft -- supply chain, spare parts, warranty, maintenance documentation, flight manuals, etc.  

Marketing has to figure how many they can sell at what price. Will it generate new sales in addition to the existing aircraft? Will it cannibalize existing a/c sales? How long will it take to recoup the cost of the change? How much will it add to the bottom line over each of the next 10 years?  

Ultimately; what's the ROI? And; is there a better place to allocate our capital for a better ROI?  

I'm guessing most OEMs found a better place to spend their development dollars.