I prefer the original theatrical version (Donnor/Lester) to be honest. The Donnor Cut is hurt by the fact that it's an incomplete film that has been edited together from scenes shot by Donnor and others by Lester to complete it. However the Jor-El scenes do help tie the movie together better when it comes to the mythos of Superman. Also the fight scene in Metropolis had some extra oomph to it. Like when Superman was sent spiraling in to the statue of liberty.
The time travel fix of things was kinda lame but I blame that more on Donnor being fired before he could finish his original film, and had to edit an ending together decades later.