I would pick Michael Bay, just to keep the tone/sillyness of the previous Transformers/G.I. Joe movie. I don't think it would be a good crossover film anyway, so they might as well stick with what they have in the past.
Out of all of the Transformers and G.I. Joe movies, I liked Jon Chu best as a director. Not a fan of Sommer, and Bay is too hit-and-miss. I wouldn't complain at all if Chu got it. Though, I would ideally hire someone like Brad Bird for a crossover.
I hope this eventually happens. There's no excuse not to. Especially since you have the Rock involved with the Joe franchise now. of course, we'll see how things get "integrated" in terms of the continuity, if at all. Could be fun.
Chu doesn't even know how to deliver spectacle, Michael Bay has proven that he liked the militar almost as much as the transformers, he's the only one who could do this job as the franchises are right now.