Fans of long-running franchises, are in general looking for obvious changes to be reconciled. It happens in Doctor Who all the time, and often in ways that neither harm the episode or cause the whole story to derail for general viewers. A throwaway at least. A whole bonus piece of supplementary drama, like a minisode... which is basically what deleted scenes are sometimes.
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But would that really have improved the movie, made it more dramatic or exciting or compelling or whatever? Would it have improved the acting or the directing or the pacing? Would it have made the slightest bit of difference at the box office?
In other words, what would it have accomplished, aside from scratching some sort of continuity itch? And in a rebooted version of the franchise to boot?
(And, yes, I understand the fictional time-travel gimmick involved. But, in the real world, it's basically a reboot aimed a new generation of viewers. And what's the point of rebooting the whole shebang if we're still going to treat the old episodes as gospel?)
Rationalizing discrepancies away is what fanzines, message boards, and novels are for!

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