It's not software, relationships, rivalries, cost, or maintenance. It's obsolescence.
By the time there's a full wing of F-35s in regular service, there will be drones capable of routinely shooting them down. The advantage of not needing to coddle a pilot and having all possible G-forces available will make even cheap drones distributed by corrupt Chinese or Russian backchannels superior to the best fighter jets in the world within ten years.
And a whole wing of such drones will soon come cheaper than a single F35.
Obama should do the same to the F-35 as he did to the F-22 and cancel it before it wastes more money.