It is your story, so you can fit whatever characters in as you like. The Sith are everywhere though, Sith stories are a dime a dozen. You want to aim for something new and unique. You don't want sacrifice story just for the sake of jamming in a character you really want to be in your story (like the Stormtroopers) if they fit in somewhere, that is great, but if they don't, do not hesitate to leave them out.

Same for Luke's son, if he fits, put him in, if he doesn't forget him. This story can take place anytime you want as well. It could be a year after ROTJ if you wanted it to be, or 20 years after. Don't feel like you have to place it at the very end of current EU continuity. Mara Jade could still be a live for you story if you wanted her to be, same thing for Chewie, by just having it take place before their deaths.