Additionally, not all characters are available right away. I.e., Darth Maul is playable in the Twilight of the Republic playset, but only after you get his Champmion Coin (which is pretty easy; it's not deeply hidden or anything). Like others have said, it's sort of like the LEGO games - play through it at first with the "real" cast and then unlock playing in the Clone Wars as Luke or fight against Darth Vader as Anakin Skywalker as you go.
I don't know if they've announced the exact details yet, but I'd surprised if they didn't let you use the old Marvel heroes. Especially since the only new Marvel 3.0 guys are Ultron and Hulkbuster Ironman (and I guess Black Symbiote Spider-Man but I think he's just a reskin).