Great point.
The 6.2 is a relatively straight forward engine design and has proven to be been very trouble free. However, that doesn't mean the 3.5 is automatically inferior just because it has turbochargers and direct injection. "Reliability" is not determined on a sliding scale based on the number of systems and parts; it comes down to design, engineering, and the quality of the components that make up the engine.
Ford didn't just slap a couple of turbos on an N/A 3.5 in 2011 and call it an EcoBoost. Even though the engine was projected to be a low volume option (opposite of what happened) it needed to pass all F-Series durability tests without failure. For those that have read Iron Fist, Lead Foot (John Coletti) you know what is required of a engine to pass Ford's most basic durability testing. Once the engine passes in that environment, it is tested in the real world under the most extreme conditions possible. If it couldn't pass, it would have been back to the drawing board.
The Gen II 3.5 was developed using all of the lesson learned from the Gen 1 3.5. They went from a mechanical bucket valvetrain (DAMB) to roller finger followers, added Port Fuel Injection (PFI) to the Direct Injection (DI) system, revised the entire timing chain design for enhanced performance and reliability, hollowed out the camshafts, upped the compression ratio, revised the metallurgy in the turbocharger compressor wheels (lighter and stronger M-247 Alloy), and adopted new electronic turbocharger wastegates.
Unless someone has empirical data that shows these engines experience XX or YY failure at 200K miles, claiming they are "unreliable" or "less reliable" is just hearsay, because there is no data to back it up. Anyone can provide "what ifs", but what actually matters is the results of real world use.
