The reason this kind of thing isn't realized, are a related two-fold reasons:
One-- retailers don't want it.
Two--retailers don't think GIJOE, as a brand, has the clout (or public interest) to warrant such a large toy taking up space on their shelves. This when there are other brands that are far more popular and sell far better that DO warrant more self-space.
GIJOE takes up so little space in the pegs and shelves that offering a $400 ( or even a $200 or $100) toy that is about 3 feet long ( broken down in the box) would be ludicrous. It exceeds the "footprint" the retailers grant the brand on their shelves.
Also, large GIJOE sets have routinely undersold and mostly gone to clearance over the past 10 years. That is a trend that retailers do not ignore. The last time was the PITT set, which was not that popular.
That and the chronic observation that GIJOE is NOT a perennial line, but a seasonal one. It sells best as Christmas time, when parents and grand parents recognize the brand name when shopping for children. The rest of the year that consumer demographic just doesn't shop in the toy aisles. Collector demographics are not a consideration because there's not enough of us.
There's nothing that we as fans can do about this.
It's market forces at play, and retailer experience and intuition calling the shots.. Hasbro and retailers are also risk-adverse.
Sure, they'll do large sets for Star Wars--because Star Wars has a consumer audience easily 100 times that of GIJOE, on GIJOE's best day. GIJOE has multiple stigmas working against it--political slights, prior brand failures, weak movie promotion/performance, weak media tie-ins ( no animated cartoons). That and action figure brands all across the board are softening in sales.
It remains a enjoyed brand, but its not enjoyed anywhere near enough for sets like the Defiant, Flagg, or Terrordrome of old to be produced today. The largest we'll see from this point on is something like the Eaglehawk or the Skystriker. That's it.
The prototype you likely saw was likely itself to just have been a concept piece. Toy makers, like Hasbro, throw a lot of stuff at the wall to see what sticks. They'll make a mock-up, show it to the retailers to see if they are interested in carrying it, and IF they get interest, it'll go into production. Otherwise......the prototype is put away on a shelf and forgotten about.
The consumers DO NOT dictate production green-lights in something like this--it's the retailers that make that call.
Hasbro does not sell to consumers, they sell to retailers. Retailers then sell to consumers. We do not factor into the equation at all.
Also, consider the "footprint" again; for a 3 foot long USS Flagg toy, means the shelf space can only fit maybe one or two on the shelf space (endcap or any part of the aisle) at one time. They can stock.......what...........50 figures in 2-3 rows of peg space, and about a dozen smaller vehicles. in about half that footprint size. At $10 a figure, and $20 a vehicle you'd be looking at 5 times the income with more visible product for sale in less space than a single showy toy takes up. And Hasbro PAYS the retailers for that space ( Walmart, TRU etc.) so they want the bag for their buck.
So, in a long-winded nutshell....that's why you'll NEVER see a USS Flagg at retail again.