There's definitely a limitation to GI Joe being a military organization and as such the stories which can logically by told about it.
That being said, it was interesting even back in the '80s contrasting the cartoon with the Marvel comic, which Larry Hama (a Vietnam vet) wrote between '82 and '94, and which used actual weapons (rather than laser guns) and military terminology, full of remarkably realistic details which were a little incongruous alongside licensed toy images.
I remember in one of the first issues I read some Central American soldiers are remarking on the raid (by the Joes) they had just survived and speculating that it must have been the Americans, because if it had been the Soviets they'd be dead, and if it was the Israelis they'd have never known they were there, or some such. Relatively adult and topical military/foreign policy humor for the day.
While the comic certainly still wasn't what you'd call realistic or mature, it was definitely much moreso. And they had the Special Missions spin off series, which was specifically written to be more mature and morally-ambiguous. The Joes being tasked with more conventional counterterrorism missions, often against real world forces or more realistic terrorists rather than Cobra.
Given some of the other surprisingly high-quality reboots we've seen in recent years, I wouldn't be surprised if one was managed with GI Joe. Although definitely the geopolitical landscape has changed a lot since the end of the Cold War, and more Americans are skeptical of the military in general than once we were.