If you want an interesting crossover, there was a Joe vs Transformers from IDW from 2014-2016. It's in it's own continuity, but shares a lot familiarity with the original Marvel runs of both series. The first few issues I thought where just weird and crap, and looked up the artist so I could rage against him. I couldn't understand why people where lauding this guy so much. Then I read an article with him about the crossover and it made 100000% sense.
So back in the day, Jake Kirby got picked to do the comic adaptation of the movie 2001. They gave him a different draft of the script to work with then the film script so he pretty much did his own thing in a gloriously bonkers way that only Kirby could get away with.
So these guys that did the crossover pretty much said "What if in the early 80's there was a film of GI Joe vs Transformers that we got picked to do the comic of, but didn't watch the movie and have no idea who any of the characters are besides a few pictures of the toys." It is so alien and strange and bonkers and it's great.
Slight spolier Flint and Lady Jay's future daughter Marissa and Brawn the Autobot get married