The only problem I have with it all is the emporer clones, as you said. The rest of it makes sense. I think ROTJ's ending shows that they'd finally won the war, but in a way, it wasn't all over yet. It never says that, but you kind of get that vibe that peace will come most definately, but there's still a few hurdles. That's why the SE f'ed it up so bad with that ending where the whole galaxy is celebrating. Killing the emporer doesn't liberate a galaxy. It's the biggest part, but there's lots left.