Crossovers were more common back then. But now they're both being grouped with a third, new comic in what's bring called the ENERGON UNIVERSE.
The first in the group is called Void Rivals and they have already featured some from the Transformers universe.
I just read a review copy of Transformers #1 (out next month). It's really interesting.
G.I. Joe is kicking off with two one-shots (Duke and Cobra Commander).