Well, they certainly could have kept the D's destruction and saucer crash-landing scene. But they could have had Picard and Kirk go back further in time to stop Soran before the ship got destroyed. That way TPTB would still have their crash scene that they wanted, and have the Ent-D still be intact at the end of the movie. But that was never the plan. Braga stated that they were just tired of seeing the D and wanted something new (the rumor that the E was built because it was easier to film is just hogwash). They could have refit it to look like it did in "All Good Things..!" Actually, that's not quite correct. TPTB wanted the actual Akira class CGI model, unaltered, for the NX-01. Their thinking was that since it was just a background ship, no one would notice that it's the same as a ship from 200 in the future. Since this was utterly ludicrous, Drexler took it upon himself to make the changes to the model to what it ended up being in the show. That's the real reason why it looks so similar to the Akira.