Skyfire is not in that ep. That's jsut random character models shown to represent a fleet (unless Powerglide has aquired the ability to fly in space). I'm getting deja vu here.
I view Wheeljack (and Windcharger) as not dieing in the move. They were just horrifically disfigured and comatose. They eventually came back later (Windcharger in Call of the Primitives) and Wheeljack in Victory (Wheeljack tacking longer to recover). I know this isn't officially true, and no doubt people are going to say "But they did die. Windcharger was only on screen for 1 second and blah blah blah Wheeljack". I don't care. This explains the appearance of those two and the change in character of Wheeljack.
BTW If they had died in the movie, why did they still have colour in their bodies? Perhaps because they wanted Prime to have such a dramatic impact when he faded. Perhaps because the only 2 to loose colour when they died were the only two to return properly (Prime and Screamer). It supports my twisted version of events, and I'm sticking to it.