Some of the concepts might have worked in different executions...a sub-unit of the Joes trained for space missions, or dealing with Cobra's genetic mutation experiments, or pollution plants - but they came across so garish and over-the-top that it's almost not even G.I.Joe at a certain point. (Robo-Joe and Bio/Monstro-Viper are probably the best examples.)
At any rate, it certainly didn't translate to the 'toon. In the comics, Cobra Commander took out Headman's drug-running because it was compromising Broca Beach, IIRC. Not out of any bizarre alliance with Falcon and a random Crimson Guard!
(And in regards to the Eco-Warriors, it bugged me as a kid to no end that Airtight didn't get a new update there. They stuck him briefly in the comics as a cameo - but really, what the heck do Flint and Barbecue have to do with the environment specialists??)