An interesting thought as to how to deal with some of the contradictions in canon. It really is a problem as things stand. Not only do you have all this non-canon material which contradicts both canon and the other non-canon material, but, in addition, the variety of Star Trek series has led to a whole lot of canon contradicting itself.
We all know, for instance, that the Klingons are cold, treacherous, and sneaky people who advance in rank by murder, but that Romulans are the "honorable enemy". Unfortunately, we also know that Klingons are honorable, ritual-bound warriors, and that Romulans are treacherous, intellectual, and Byzantine plotters.
Now, LUG did a good job of coming up with ways to reconcile all of these disparate bits of contradictory information. In fact, they did better than anyone I have ever read or heard of, including Paramount itself.
But it was, in my opinion, still not quite enough to be completely successful. And now, with a new, Braga-produced series coming down the pike, we can be sure that canon will become hopelessly self-contradictory. Soon, there will be no way to make a coherant universe out of Star Trek, no way at all.
What is the solution? Series specific canon. In TOS, the Klingons are villainous, and the Romulans honorable. In TNG, the Klingons are honorable, the Romulans Byzantine, the Borg the ultimate enemy, the Breen a mystery, and the Ferengi a threat. In DS9, the Dominion is the ultimate enemy, the Breen a major power, and the Ferengi lovable rogues. And so on. The various Star Trek universes are related, but not the same, even when they are very similar.
This is even more true when the different axioms of different series are taken into account. While the worlds of TNG and DS9 resemble one another, for example, it is very difficult to reconcile the clean, utopian Federation of TNG with its gritty, paranoid DS9 counterpart.
Note that it not including Voyager, as it contradicts itself......
This would mean that the new series will not be a problem as long as it is not self-contradictory. It will merely generate its own "Enterprise" canon, its own Star Trek spinoff universe.
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Slan agat!