Max, Amy, and Ned are driving old cars and want new ones. Rather than buying three cars, they decide to go in together and buy one car to share.

Max wants to replace his offroading jeep, Amy wants to replace her fast sports car, and Ned drives an amphicar because he lives on an island.

So Max Amy and Ned go to GM and say "Design us a floating, offroading, sports car please we are trying to save money."

By the end of the day GM has to convince them to take three variants of the same car, but the cost, time and design tradeoffs needed to reach that point were never worth it. When you could have designed three (possibly four) vehicles separately that each excel in their focus area.

Saying that 'well all three would need gauges and windshields anyway' isn't a compelling reason to combine them.

They don't have the kind of assembly commonality that the program aimed for initially, but I think it's a stretch to call the three variants "very different" aircraft. There's a pretty high amount of systems similarity. And pilots don't have to go through completely separate training programs for the three variants, just separate qualifications for things like STOVL or CV operations. If you can aviate in an F-35A, you can aviate in the other two variants.

Not sure why you single out the USMC for developing the helmet mounted display, because the HMD is common to all variants and is already a working system.

Because in real world costs tend to grow exponentially with complexity.