There's other options no one seems to be considering.
I really don't see how any of these other options would improve the films and resolve plot holes. Let me explain.
If you want to make Superman, Superman II and Superman Returns, you could always re-edit Superman so that the movie ends how they originally planned it--he catches the nuke, throws it into space, and ta-da. Then Superman II can end with the world turning back, and Superman Returns can continue.
This negatively affects S:TM in that it removes its climax. Without the emotional climax of Lois' death and Superman's actions to reverse it, the film would fall flat. Superman just stopping the missles is not a satisfying conclusion. The original creative team understood this, which is why they decided to steal SII's planned ending. Sure S:TM can be edited so instead of Lois dying, Superman just lands by her trying to start her car, but it would be a very dull way to end the film. The suggestion of leaving the timer reversal in SII brings me to your next point...
OR: You can just leave the world turning back in Superman II. Superman Returns still follows perfectly, check this out: Just because time has turned back doesn't mean Lois is no longer pregnant. In the silly version of "turning back time" that happens in this film universe--everything goes backwards, but Superman. Otherwise, when he was done, there'd be an additional Superman there on earth. So since Super-sperm can't jump out of Lois and back into Superman--the kid is STILL IN THERE after he reverses time all the way back to the end of Superman I. He leaves, she gets pissy, hooks up with Richard, and the kid that was already inside her, she just ASSUMES it's his.
Superman reversing time at the end of SII would negate all the actions of the film. True, the "science" of the time travel in these films is flawed, but we just have to accept that when Superman reverses time, it resets events to whatever point he travels back to. This is the ONLY "advantage" to Superman reversing time at the end of SII is erasing Lois' knowledge of the secret. However, replacing this with the SuperKiss takes care of this plot point, and avoids creating the following issues:
-Lois and Clark's conception of Jason: It doesn't matter if Superman's sperm was still in Lois before he reversed time. The time reversal negated that, just as the time reversal in S:TM negated Lois being dead. There was no other opportunity for Jason's conception to happen, regardless of Singer's apparent suggestion of it happening he night of Lois' first interview with Superman.
-Luthor's knowledge of the Fortress: In SR he knows where the FoS is, and how to use its controls. Without his actions in SII, there is no precedent for this.
-The three villains: How does this affect their release? The rocket Superman threw into space in S:TM is still out there and will still release the villains. Does Superman just think he'll be more prepared this time? Ironically this is only a problem in Donner's II, as in Lester's II it was the Paris bomb that released Zod and co.
-The diner bully: This is the real kicker; regardless of whether you want to acknowledge SR or not, this is a glaring plot hole that exists in the Donner Cut of SII. When Clark shows up at the diner again to teach the bully a lesson, everyone recognizes him and he explains that he's been "working out." With the time reversal, no one should know who he is, his explanation would make no sense, and of course this would be a totally unprovoked attack on Clark's part.
OR: You can just leave Lois on the balcony, and Superman trusts her. And then he leaves, she feels betrayed, and finds a man rather quickly, and convinces herself that he's the father, not Superman. That makes interpreting Lois' actions part of the scheme, though, because then her "act" that she doesn't remember Clark is an act, indeed, for the public. That might be too much of a stretch though.
This would have been an ideal way to play things if Singer had presented us with a relationship where Lois knew Clark's secret. But unfortunately he didn't; if she did that would definitely have been something the characters addressed.
But I don't understand why you NEED the magic kiss if you're going to try and link Superman II to Superman Returns. Since Donner has moved Lois and Clark's sex scene to before he depowers, and then runs the world backwards, reversing everything BUT the fact he has his stuff in her, due to the rules of time travel in the film, she's still pregnant and doesn't know he's Superman. That sets up Superman Returns pretty perfectly. AND, Donner even hints in his cut that Lois MIGHT get an inkling, later. Which she does--and it all might come flooding back to her in the sequence where she leans over and whispers to him what's up. She remembers it all, finally, even if it didn't happen anymore after he turned the world back.
We'll just see about that...