Also...Vader captured? Really? I don't think that even in these days of Star Wars expanded universe garbage would Lucas/Lucasfilm/Lucasarts allow the big bad villain and central focus of the entire saga just be neutered and captured.
Well, regardless of what it is, that is what happened. Really, a clone of Vader? Sorry, but that's a little ridiculous.
Still, I admit that the alternate ending is for a change more
compatible with the rest of the canon - the only loose end it leaves is one Starkiller clone (as opposed to up to two clones, Vader captured, and Kota alive).