I liked the Donner Cut too but like most ppl here, I'd like a Donner/Lester hybrid as well. For one thing I felt the Donner cut did not concentrate enough on the Superman-Lois romance compared to the Lester version. Those parts of the movie felt rushed and incomplete.

I don't like the ending in either version though. I think it'd be much better to have Lois remember at the end. Maybe end the movie with the Clark and Lois kiss like in the Lester version. Cut out the part where it's obvious she has forgotten everything and go straight to the diner scene.

As for the villains, I have an idea though I'm not sure if it'll work: is it possible to show that Zod and co have been banished back to the Phantom Zone by Superman? Maybe show them in that crystal floating away in space. About Lex, this is a long shot, but how about using the end of Superman IV where Lex is taken back to prison and Superman says "see you in twenty" ? I haven't seen IV in a long time so I dunno if that scene can fit into SII. Just a thought.

I don't think it's a good idea to tie this to SR. SR is supposed to be a "vague sequel" anyway. So let it remain in it's own continuity.