IMO, the sophistication of the final worm that made it out to security researchers doesn't have anything on the process that must have been used to develop it. Take the normal iterative development process, except that:
You don't know anything at all about the design of your targeted system and networks.
Even getting a little information about it requires writing sophisticated malware, using various spy capers to get the malware near the target systems, and somehow exfiltrating data from airgapped systems over the internet, where the whole mission is blown if anyone detects your data movement.
You may need dozens of iterations of adjusting the software to try and dive a little bit deeper, getting it snuck into the target systems (hopefully by a built-in update over the net), gathering information on the network architecture, then exfiltrating that data back out.
Always a tough balance of spread-happy enough to infect highly protected airgapped systems in a top-secret facility, but not so spread-happy to get out on the open net and infect half of the world, where it will inevitably be discovered eventually. This is probably where they eventually screwed up.
How long to detect that they're using this particular model of PLC with this particular centrifuge, buy your own copy of them, dig up someone who actually knows about these things, collaborate with them to figure out a sneaky way to screw things up just a little bit, build ways to get your virus onto the target system to do its damage, etc.
I'd assume that there was a team somewhere with a big library of zero-day exploits and a bunch of ace developers, but no starting knowledge of the target. Someone gave them the order to figure out a way to hack and screw up the Iranian nuclear program, maybe with the helper that some other org has a guy that can deliver any product near the program. They must have spent years devising ways to get in, slowly gathering info about their target, figuring out a way to achieve the assigned goal of screwing things up without getting detected. Now that would be a hell of a project to work on.