That idea of a long lived bad guy who first deals with the TOS crew, and then later on with the TNG crew, would have been far better. Kirk and Picard wouldn't meet in person, but that wouldn't have been necessary at all. You could mirror Kirk's struggle against the bad guy with Picard's struggle against the bad guy, with a different outcome because Picard studied Kirk's reports on the bad guy. Similar to how they mirrored Luke's fight against Vader and the Emperor with Anakin's fight against Saruman and Palpatine. And don't get me that "But the audience would have been confused" bullshit. They wouldn't have been.
And you could still have Picard and Spock meet in person. And they could have intertwined both stories using flashbacks. But that kind of storytelling wasn't really prominent in the 90s.
Heck, have the final fight in some sort of time displacement thing, where Picard and Kirk actually do meet and team up in their fight against the bad guy and create a predestination paradox. So eventually Kirk and Spock always knew that they would win with the help of some Captain from the future, but he also knew that it would take a lot of time.