GI Joe is one of the more frustrating properties, with perhaps one of the more counterproductive fandoms. Steevy Maximus has summed this up better elsewhere (but I think that may have been pre-Allspark outage).
The property at large was one of those that got sidelined in the late 80s/early 90s in the TMNT/video games/etc wave that displaced 80s franchises, and came back in the 2000s with a more adventure-y, science fiction-y bent. This is something that it needed very much, if only to create a "new" (quote marks because it had always had science fiction elements) basis for the brand as the military angle had lost a lot of ground as a selling point since the 80s. But seemingly every step of the way, the fandom got in its and the brand's own way, complaining about neon and ninjas (cool band name) and tech suits and getting away from the "roots" and other such hoopla. Where Transformers' fandom embraced the brand warts and all, GI Joe's seemed determined to do the driving, and only toward a specific direction, mass market be damned. Surprise! The brand needs the mass market. (This did draw my attention to emerging corners of the fandom that sought to be more positive, and to this day I think back to Toys and Tomfoolery and newer blogs like The Dragon Fortress with fondness.)
This would persist into the movie era. Its live-action efforts failed where Transformers' somehow succeeded. But the line kept going, with incredible, cool, quality toys that... didn't seem to do much to move the needle for the brand as a whole however well it catered to those same old tastes. The brand was further held back by Hasbro's Hub era, and some weirdness around the release of Retaliation, then ... The brand as a whole seemed to just go quietly into the night.
Even in the 2010s the natural/understandable automatic question of a Joe/TF crossover seemed like using Transformers to prop up essentially a ghost of a brand, and that's even more the case now. That tease fell completely flat with me at the end of ROTB because of that (and because I felt the Transformers movies themselves need some propping up of their own).
There's a lot that CAN be done with the brand, I feel, and different viable directions to go in (outside of essentially NEST Again). I do hope it gets some media that catches fire with the new, young/diverse generation of viewers it needs.