Honestly, I thought the structure was fine, and I'm not sure that anyone's come up with a better one.
Prelude in the TOS era with Kirk setting up the main macguffin, then the TNG cast picks up the story before bringing Kirk and Picard together for the climax.
Having Kirk and Picard meet was the whole hook for the movie. It absolutely worked for the marketing department, leading to Shatner and Stewart on the cover of Time Magazine. Star Trek's arguable cultural zenith.
The issues with the film are all the bits around that - mainly the unclear and confusing nature of the Nexus, the limp subplot with the Duras sisters, leading to the unearned crash of the Enterprise-D. And Soren being a villain who just didn't quite work, despite the great casting of McDowell.
I've toyed with the idea of a non-linear cut of
Generations, moving the prologue to the middle of the film after Riker says "That's the mission where James Kirk died," except I don't know exactly where it goes, and I'm not sure it makes anything better.
Soran as a villain is a problem. Picard is far more of an obstacle for Soran than Soran is an obstacle for Picard, and from Picard's side their conflict feels rather stakes-free. What I mean by that, since the
Enterprise-D crashes and is destroyed, is that Picard doesn't know this. He and Soran are having a monkeybars fight with the lives of millions we never, ever see at stake. We in the audience need to keep this is mind, but it's not really concrete to Picard in the film. The stakes, even the D crew, are abstract in what we see from Picard's POV.
I realize it would be a big honking coincidence -- planets are
huge -- but I'd have had an establishing shot of Picard seeing the saucer streaking through the skies above Soran's base. Picard's ship is gone, his crew is likely dead, it's all up to him.
I'd have worked Soran into Picard's Nexus fantasy in some fashion. Maybe Soran and his family come to Christmas dinner at the Picards, and Picard in his Nexus confusion feels that Soran is a friend but also feels a sense of unease, and Soran says some things in their dinner conversation that seem pleasant but have an undercurrent of taunting and menace. I now imagine a conversation about the "Picard who fought at Trafalgar" (which has always been strange to my historian-self, as the French were utterly routed at Trafalgar, so why is Picard so proud of that?), and on the surface it seems fine but the undercurrent is that
this Picard also lost his ship and his crew.
Also, if the Nexus can take one to any time and any place, there are other places Kirk and Picard could go. And maybe the climax of the film takes place in Kirk's time, on the B.
I also think that they could have done a
Deep Space Nine episode that connected in some way to
Generations, much as "Unification" connected to
Star Trek VI. Mark Altman did a comic for Malibu with the Duras sisters looking for trilithium, so maybe something like that would have made the film feel "bigger." Soran visits DS9 or something like that. Why not?