I would have ditched the whole concept of the Nexus altogether and just have it be a situation where the villain was a long-lived baddie that caused trouble for Kirk and his crew during the first half of the movie and then returned to finish what he started in the second half nearly a century later, running into Picard and his crew at that time. It definitely would have been a half-and-half movie divided between the 23rd-Century and the 24th-Century.
Yeah, there probably wouldn't have been a direct
meeting between Kirk and Picard that way, but there would have been a scene in which Picard is accessing Kirk's report on the baddie on the holodeck. So we'd still finally see the two captains together in the 24th-Century, but via an interactive holodeck program in which the Kirk hologram talks to Picard the way the real Kirk would.
Other stuff I'd done:
- We still would have seen the launch of the Enterprise-B, but with Spock and more of the TOS cast aboard (don't know if DeForest Kelley would have returned since he was apparently happy with how things ended in Star Trek VI).
- Rather than destroy the Enterprise-D, she would have been severely damaged in battle, perhaps even losing an entire nacelle and a big chunk of her saucer section. That would ultimately pave the way for an upgraded and redesigned version of the ship for Star Trek VIII (like how the original Enterprise was for Star Trek I).
- We would still see the Duras sisters as the main baddie's minions.