I think it's too soon to do a Transformers/GI Joe crossover film.
Let GI Joe have its own shine. Ironically, Michael Bay would have been the perfect director for a GI Joe series of films.
I liked Rise of the Beasts but I feel its' time for Transformers live action films to take a break for at least 5-7 years, giving GI Joe a chance to have a successful run of films before doing a full on cross over.