The Transformers film franchise has been box office gold since the beginning. However, the other film series based on classic toys, G.I.Joe hasn't done nearly as well. One director had the idea to help boost the latter by adding the former. D.J. Caruso was previously attached to direct a third installment of the G.I. Joe franchise and while that film has yet to materialize, it turns out that at least part of the reason is that the director had an idea for the film that Paramount wasn't yet ready to pull the trigger on, add the Transformers.
Well yeah but they're not ready to do [G.I. Joe meets Transformers] yet. That's exactly what they should do but they're not ready to do that because in fact the script that I was developing, the two worlds sort of collided at the end and when they read it they were like, 'We're not ready to do this yet.'... They will eventually collide those two worlds and it's probably when Mr. Bay decides he's done with Transformers.
D.J. Caruso went on to direct xXx: The Return of Xander Cage instead of working on a G.I. Joe 3. However, he tells Collider that he will probably be speaking with Paramount about G.I. Joe again now that xXx is wrapped up. The fact that Michael Bay is claiming the next entry in the Transformers franchise will be his last could even mean there's still a chance of something like this happening down the line.
Several months ago Paramount put together a story team who was going to work on ideas for films involving several Hasbro toy lines. G.I. Joe was one of them, along with M.A.S.K., Visionaries, and others. At the time the word was that Transformers would not be part of this "Hasbro Cinematic Universe" as there was already a team assembled working on sequels and spinoffs for them. If this team already has some good ideas for the future of G.I. Joe that don't include Transformers, then they'll probably be going ahead with those.
Many would probably agree that combining the two franchises together is exactly what they both need. G.I. Joe would clearly get a boost from adding the Transformers, and Transformers could use the refresh of adding some new blood like G.I. Joe. While it's been awhile since the last G.I. Joe movie, most would agree that the sequel did improve on the lackluster original. D.J. Caruso himself says that the series just hasn't been able to click yet. Maybe it's because it's been missing giant robots. It's not like there aren't already some pretty impressive soldiers within the Transformers movies who could act as the link between the two universes.