The original Flagg's deck is lost, it is the largest and most significant part of the toy, and is too expensive to make new molds for - so no, the Flagg will never be re-released according to the Hasbro toy engineer who designed it (or at least tested it by standing on it) - this was explained to me first hand and became a topic of conversation between JC members and Hasbro staff at the bar during the Atlanta convention.
Certainly things could change over the years but the original Flagg was a poor seller in the first place and only released in the first place as a Trojan Horse marketing ploy to convince the buyers who were skeptical about GI Joes success that Hasbro believed enough in the toy line to risk something like a 7.5 ft long toy. The ballsy move worked then. But todays market doesn't placate such actions. The original Flagg would take up more shelf space than the Millenium Falcon and cost twice as much.
Now the new cartoon has a new Flagg in it and there was speculation (photos?) that a new, smaller, Flagg based on that design may be released one day.
Personally I'd prefer something more LHA size using the cartoons split-V runway design and a launch for the Whale on the back.
LHAs:
http://www.defenseindustrydaily.com/the ... ated-0870/