Here's what I'd do to fix the Nexus story...
1) Improve the Enterprise-B prologue. Up the stakes in a more believable way than the dumb "X won't be here Tuesday" thing. Get rid of the stupid TNG-style technobabble that doesn't belong in the TOS movie era. ("Channel the BS thru the main deflector dish to simulate a tractor beam", etc.) Rewrite Scotty & Chekov's dialogue so it's organic to them instead of obviously reassigned Spock & McCoy exchanges. ("I have a theory"/"I thought you might" and "You and you, you just became nurses" being the worst offenders.)
7) Either give Kirk a death worthy of him, or just forget about it altogether. It bugs me that Kirk dies in the 24th Century and none of his friends from the original Enterprise in the 23rd Century have any idea what REALLY happened to him. And Spock and McCoy aren't even there. (And please don't trot out the "I've always known I'll die alone" line from STV. Kirk isn't psychic so we shouldn't treat that as some prophecy to be fulfilled. It's just Kirk having a melancholy moment, he is wont to do.) After nearly 30 years of Star Trek, Kirk dying should've been one of the biggest events EVER. Instead, the film expects us to get more broken up about Data finding his damn cat at the end of the movie.
The way to fix the prologue, imho, is to make it more than just a teaser and have it actually be an integral part of the film. You can cut the prologue and you don't really lose anything. And so if I were doing a page one rewrite, I would connect the prologue and the climax by staging the climax on the
Enterprise-B itself.
First, increase the stakes. Picard sees the
Enterprise-D saucer cutting through the skies above Soran's missile while they fight on Veridian III. Picard believes his crew has died.
Second, I would make Soran a little more sinister. He's Picard's Christmas dinner guest in the Nexus! Picard's wife knows Soran as an old friend of the family, but he unnerves Picard and speaks of his (Soran's) dead wife and how he wishes he could save her. As they talk, he says something that begins to snap Picard out of his deluded haze. Then Picard sees Guinan, and he realizes what's going on and what he has to do. Which leads to Kirk...
...and as he and Kirk talk about what's at stake and what he (Picard) has lost, Kirk has a better idea than going back to Veridian III. What if they went back to the
Enterprise-B instead and dealt with Soran there? Picard's
Enterprise won't be lost.
Third, when we get back to the
Enterprise-B, Soran "sensed" where Picard had gone and followed him out of the Nexus to stop him. He seizes Engineering and tries to force the ship into the Nexus, and Kirk and Picard try to stop him. They fight around the warp core. There's a warp core breach, but the locks to eject the warp core are jammed. Kirk manually flips the locks, but this means he'll be ejected from the ship along with the warp core. Kirk is able to complete the lock sequence, blast doors drop down sealing him and Soran off from the rest of Engineering, and Picard watches as Kirk and Soran are pulled out into space with the warp core. The resulting explosion kicks the
Enterprise away from the Nexus and all is saved. Then Picard fades away because the timeline he's from no longer exists.
Picard wakes from a nap on the
Enterprise-D with a dream that felt so real. He has a message from Rene about something (butterfly effect -- he and Robert are fine). He goes to Ten-Forward, Guinan senses his confusion. He tells her he remembers someone -- an enemy? a friend? -- telling him "Time is the fire in which we burn," but that couldn't be real, and she tells him that all that he experienced was real, that time works in mysterious ways.
I'd ditch the idea of the Nexus and the fanwank(ish) desire for Kirk and Picard to meet and fight side-by-side. It's really enough that they would be in the same movie, IMO. Instead, the plot would revolve around a long-lived adversary that Kirk and the crew of the Enterprise-B defeated in the 2rd-Century, but would later escape incarceration and become a problem for Picard and the Enterprise-D in the 24th-Century. There would be a scene in which Picard would review Kirk's personal logs and see a recording from the man himself. Picard would use Kirk's insight of the adversary to eventually defeat him.
That's essentially the premise of the Maurice Hurley script. There's an enemy from another dimension threatening the Federation in Picard's time, and he consults with Kirk on the Holodeck about the events of "The Tholian Web."