Kevin Smith can pretty much do whatever he wants. He decides that he wants to direct an episode of Battlestar Galactica, so they let him. He wants to create a character and write an episode of Heroes Origins, and they let him. That's a lot of clout, friends. So, what can we expect to see from such collaborations? Well, at least on BSG, likely not much that you'll notice out of the ordinary, since Smith admits that there's pretty much a formula of what to do on the show, and he's not going to deviate much from it.
Now, Heroes Origins, on the other hand, is a whole other ball of wax. They've given Smith the run of his episode, allowed him to write and create new characters, and pretty much do whatever he wants to do. So, will we be treated to two superheroes standing around in a mall talking for an hour? Who knows, but it should be worth the watch.