Both cuts are severely flawed. The Lester Cut, as others have mentioned, is the only one that feels like a polished high-budget movie, shot and completed in the 1980s.

The Donner Cut, however, still remains my preferred version. Though somewhat rough, it makes crucial changes.

Having the villains be released because of the missile from the first film gives his climactic turning back of time from the previous film necessary weight. Intentionally or not (more on that in a second), it retroactively justifies Jor-El’s warnings that such an act is forbidden and punishes Superman for his well-intentioned transgression. This is all undermined if the villains were released by a random bomb. That being said, the ending of the Donner Cut makes it seem as if the creators were unaware of this bit of subtext, as he does the same thing… Honestly, just leaving Lois knowing Superman’s secret identity would have been the best solution; as she outright states in a beautifully heartbreaking scene, she’ll keep his secret.
Marlon Brando being back thematically continues the first film (Father becomes the son).
Gene Hackman is Lex Luthor for the entire film and not some painfully obvious stand-in, who is dubbed in a way that is equally painful and obvious.
No random Kryptonian powers (except for turning back time).
Much of the goofy humor inserted by Lester is thankfully excised, making Zod and his followers far more threatening.
Donner just seems a superior director of actors for the material, though, in fairness, Lester was just dropped in a production that had already spiraled out of control. But, just watch the balcony scene between Lois and Superman near the end of the Donner Cut and tell me the Lester Cut has any fresh scenes directed remotely to that level of quality.

Of course, the Donner Cut does suffer from the awkwardly written and shot Blank Bullets reveal scene (which somehow manages to be weaker than the middling Pink Bear scene with its half-assed psycho-babble), an overall weaker score with reused John Williams music, and subpar, underfunded early 2000s CGI Special Effects. The BD transfer, taken from the 2006 HD master, is undeniably weak in contrast, color, and detail; the newly minted transfer of the theatrical cut wipes the floor with it.

Honestly, the best version I’ve seen is Booshman’s. It thoroughly mixes the two cuts to create a satisfying hybrid. Clearly, Booshman knows the movie very well, in order to choose exactly t The only drawbacks are a few overt digital effects, which, though well-intentioned, do stand out. Additionally, video quality, while nice for the time, is left somewhat weak looking because it was culled from the SD version of the weak Donner Cut master and the aged theatrical cut DVD.

Luckily, Booshman is working on a new HD Version that I have no doubt will be absolutely remarkable. His new special effects integrate more seamlessly than his old ones. It will be a great day when that version of Superman II is finally released.