My personal opinion is that GI Joe needs to embrace the Adventure Team aspect as the military one is just too controversial these days.
You can still have Cobra as the villains, you can even have them affiliated with the US government. But you gotta get away from the reliance on the "US military or nothing" mentality.
I've been saying this for years upon years now. (Been meaning to write an article on the idea, too.)
Basically since MTMTE/Lost Light was a thing.
It's like, basically do that, but with GI Joe.
And before anyone says anything, I don't mean literally just doing that, but use it as a template of how to take a war-based franchise past its war-based roots and still keep the conflict and entertaining aspects. Doesn't have to be the same tone or high jinks or whatever.
And hey, as noted by invoking Adventure Team, this is something GI Joe did first, long before MTMTE or even ARAH.
I'd make the lot of them ex-military, brought on by a secret organization to _________. I dunno, fill in the blank with some sort of quest, objective, Macguffin hunt, whatever, all across the globe. But there's the reason for your military-ish namedrop without them being military.
And there are ways to go about the Cobra aspect. One is to make the Joe/Cobra conflict, as we know it, sort of the backstory behind both sides.
Or have many of the major characters sort of be their own faction. Cobra, Destro and MARS, Major Bludd and his guys, Zartan and the Dreadnoks. Lots of room for teaming up and backstabbing. Each with their own goals and reasons for going after whatever they're going after.
I think part of the reason they switched back to Bay style after BB is because the BB movie wasn't exactly a huge hit in cinemas and thought to go back to the Micheal Bay style with some character development for the TFs and giving them actual roles, but in the end, they end up killing the villians again, which is part of the reason that the movies are going downhill, they add big name characters only to kill them off in the same movie and not really work with the established TF lore that has been built up, but then, I'm a little tired of the Allspark being a object that the two sides fight over or generally having a mcguffin to the plot as that started in serious with the anime TF series, when just trying to obtain energy, seemed more intersting, thou I highly doult they'll stop doing that
Oh, I've said this before, but I am SO TIRED of the Allspark being the sole reason Transformers seem to go to war any more. At least it feels like we're getting away from that.
Earthspark mixed it up a bit, and I guess RotB did, too. Make energy a thing again for an outing.
Hell, these days, you could probably get away with some play on class warfare by making Decepticons the entitled elite (sort of flipping the more recent origins of Megatron on its head, though he could still be that and forget where he came from), and Autobots the lower-class guys trying to step up and keep the rich assholes from ruining everything for everyone everywhere.