I think there's a key difference between the Turtles and GI Joe/MotU, which is that the Turtles are fundamentally kind of edgy and gross and weird and also weirdly relatable to kids. They're freaks from the sewers, who got changed by goo, who like pizza, and even right there, you've got something fundamentally more likely to appeal to a kid than some nonce in a dubious military uniform or a gurning, be-muscled barbarian. It's not that kids won't ever see the latter two types as cool, it's just that their appeal is more temporally limited, both to the era they're created in, and to the kids themselves, who are later on much more likely to be embarrassed by having like MotU than they are TMNT.
I think you can see this in the way no reboot of GI Joe has ever really succeeded, whereas with Turtles reboots, the question mostly is how well do they succeed.