Shepard doesn't die in the best ending.
Also your crew are on the Normandy SR2 because you went to the final mission alone, Joker and your crew fled - hence why they are on the other side of the galaxy. (and yes, its a retcon on what happens 5 mins before the ending, but they also retconned the entire lore about the reapers in the ending so it shouldn't surprise you too much.







