Most of the reception to Duke #1 and Cobra Commander #1 seems to be pretty positive
Although interestingly, there are complaints from both ends of the TF/Joe fandom. The Transformers fandom is worried that the soldier toys will take over the storytelling due to bad memories of the Michael Bay movies and the later IDW years when IDW tried to barnacle every franchise they had to the Robots in Disguise in the vain hope of trying to sell them again (and as such series' as Transformers vs Visionaries showed, utterly failed). The only reason we never got Transformers/Jem was because Jem sold so poorly that IDW was forced to cancel it despite fear of social media backlash.
Meanwhile, GI Joe purists seem upset at the presence of Cobra-La, an ancient society of biotechnology using humanoids and how it runs completely contrary to the brand's "realistic tomorrow" idea, where the heroes and villains are using next-generation military weaponry, but nothing that would fall into the realm of science fiction, something that both Duke and Cobra Commander seem to be embracing.
All that being said, I think the circumstances are very different and that the Energon Universe, while ambitious, is working really well so far and has the potential to continue to be amazing.
IDW rammed the Joes into the Transformers midway into both of their runs, when the status quo of both franchises had been established. Saying that the ensuing mixture did not work was probably the best way to put it, as Revolution was critically panned and viewed internally as a failure, putting the kibosh on a shared Hasbro universe when the company was desperately hoping to match the then-seemingly unstoppable Marvel Cinematic Universe. The Joe fans didn't want the unstoppable robots making their army men feel less important, and the Transformers fans didn't want more armed forces fellation that the Bay movies were accused of. And neither side wanted the plot to completely stop for ANOTER Hasbro license like the Visionaries, a toyline that bombed when it came out, or Jem, a series that sold terribly but IDW refused to cancel out of a fear of social media backlash due to it awkwardly tackling issues like body positivity and having numerous canon LBGTQ+ relationships, only canceling it when it was clear they couldn't prop the license up anymore and having to eat the bad press.
The Energon Universe, meanwhile, is being built from the ground up, with the connecting pieces being put in much more smoothly. Furthermore, by building out the world, it feels like Skybound can avoid a lot of the bigger issues with the franchise. With the Transformers, IDW2 bombed due to a lack of any grounding human element, so the robots felt less special than they should have. With Joe, the sci-fi flavor and government conspiracy angles play a lot better to a modern audience than straight soldier toys, something that's a lot less popular in 2024 than it was in the decade of decadence.
I'm sorry for the ramble, but while I get the trepidation, I think in the end, the Energon Universe has the potential to make the franchises feel greater, not lesser, by combining smoothly, and only having Transformers, GI Joe, and the Void Rivals covering three aspects of the universe, without worrying about the Visionaries or Jem showing up and awkwardly derailing the plot.