Re: Director's Cuts that are actually improvements
The Donner Cut doesn't reuse the ending, so much as put it back where it was supposed to be in the first place. It was never intended to be used in the first movie.
The reason the time travel ending is superior to the kiss ending is because of the huge difference in motivation. The basic premise of Superman II is that Superman abdicates his responsibility to protect all the people of the world. The consequences are disastrous. First, the Kryptonian prisoners seize Texas, then the United States. We can logically assume that they plan on taking over the whole world, after their brief detour to the Fortress of Solitude. Putting it lightly, these guys caused a lot of trouble.
Superman could not allow this to stand. He made a dreadful mistake and the costs were astronomical. So he traveled back to a point where he could right what went wrong.
This does not negate the movie, because the entire point is that he must make the hero's choice: leave everything the way it is and attempt to salvage his chance at love, or destroy his chance at love so that the world may live in peace. He has only the memory of his brief time with Lois to carry with him for the rest of his life. He can never talk to her about it, and he can never otherwise unload his terrible burden.
The kiss ending seems to miss the point. Superman defers his chance at human kinship, but the world is still in a shambles. It really is just a quick and dirty way of resetting his relationship with Lois to the status quo, without any greater effect. Not only does this seem to overlook any sort of heroic motivation, but it also sets up a huge logical failure: what happens when Lois goes outside and sees the apocalyptic results of what was happening during the time that she can't remember?
By tacking the time travel sequence onto the end of the first movie, it really does come off as more of a selfish, "emergency reset button"-type move. In this case, I would argue that JB's criticism is valid. But, again, it was never intended to be there, and was only put there as a result of executive meddling.