1. Destroying the old Star Trek Expanded Universe: I know this was motivated by all of the changes to canon by the new series but I kind of regret it the same way Crisis on Infinite Earths blew up so many beloved alternate Earths. Fantastic series but depressing all the same.
I wish people wouldn't co-opt
Star Wars's "Expanded Universe" label for Trek. It implies that the two tie-in continuities worked the same way, which is grossly misleading. In the
Star Wars EU, all tie-ins across prose, comics, and games were treated as a single unified continuity, even trying to mash in older stuff like the early Marvel comics that was no longer consistent with a lot of stuff in the movies. In
Star Trek, there was never a single overarching continuity. The Novelverse was just one of multiple independent continuities. There were other novels such as the Shatnerverse that weren't part of it, there were separate game continuities like
Star Trek Online, and there were comics set in various continuities, with a few Wildstorm and IDW comics set in the Novelverse (or retroactively absorbed into it) but most of them in separate continuities.
In short, continuity was mandatory in the
Star Wars EU (and in the new continuity that replaced it) but has always been optional in Trek tie-ins. I think it's easier to accept the Novelverse coming to an end if you remember that it was never the only tie-in continuity, just one of various options.
3. Killing off the Borg in Destiny: It was the perfect capstone to what would have made a fantastic set of episodes but I feel like it also was uncomfortably removing a pillar of Trekdom. Mind you. I was shocked that they chose to go with the Borg being gone in Picard too.
That's because there's not that much you can do with the Borg, and doing too much cheapens them, as
Voyager audiences came to feel.
4. The Typhon Pact NOT Being Evil: This is something that will probably be the most controversial statement but it always stuck with me an author explaining that the point was not to create a villain faction but show an alternative to the Federation as well as expand on the factions involved. Which fair but they're mostly a bunch of authoritarian anti-democratic groups with imperialist ambitions.
But that's the point. The intent was to draw an analogy with the formation of the Federation. Look at
Enterprise, where Vulcan and Andoria were imperialist military states at war with each other and the Tellarites didn't seem much better. None of them really looked that much like "good guys" at the time, but the story was about how they grew into something better. The intent of
Typhon Pact was to explore how a loose alliance of self-serving governments came together and whether they would fall to their baser instincts or recognize the benefits of cooperation and evolve into a better society, as the Federation founders did.
And really, if you pay attention, the main thrust of the Typhon Pact novels is not about the Pact vs. the Federation, but about the jockeying for power between rival factions within the Pact. Or even within single Pact members, like the internal conflict between the two Romulan states or between the theocrats and reformers among the Kinshaya. The story wasn't about evil black-hatted villains menacing our clean-cut heroes, it was about exploring the turbulent sociopolitical process of a nascent alliance among powers who were not naturally inclined toward cooperation.
Time travel rules meantime are constantly being revised based on the writers and producers and executive teams involved. Days of Future Past and Endgame both somehow exist in the greater Marvel filmic multiverse, meantime - but both present pretty contradictory time travel models. The difference being maybe that Wolverine literally 'held two timelines in his head', and so was some sort of arguable bridge of the two streams...
Oh, good point, I hadn't thought of that. See, this is why I don't like it when different SF/fantasy universes that were written with different rules and worldbuilding are mashed together as a "multiverse." Physics isn't multiple-choice. If there is a multiverse, then the same laws would apply in every timeline.
Yeah, the Supernova was something I was looking forward to being handled for years before Coda happened. Props to Doctor McCormack for doing the fantastic THE LAST BEST HOPE novel that I wish had been the pilot for the Picard series (because I have Q's powers in my imagination).
But I admit the movie version is so silly that it would have probably been two chapters of trying to explain why Spock can outrun a shockwave that will consume the galaxy or suck up the blast of the Supernova given its traveling at Lightspeed and likely to end at the end of the system.
Still, I can't imagine that KRAD and Christopher haven't had to make sense of worse.
I actually thought
Picard's reinterpretation of the supernova was much better than the handwave I would've offered in the books given the chance. I would've been stuck with the movie's implication that the supernova happened without warning in a different star system and somehow propagated FTL, reaching Romulus faster than predicted. But since PIC was canon rather than a tie-in, its creators were freer to take license with the details. Their retcon that it happened to Romulus's own star and that there were years of advance warning made so much more sense than what the movie implied. (Aside from the fact that habitable stars don't go supernova -- though they did several times in TOS -- and that there'd realistically be millennia of advance warning.)
The one thing that doesn't make sense is why Spock would still have tried releasing the Red Matter after the supernova already blew, but maybe that's another thing the movie was misleading about and the supernova actually happened just after he released it but before it activated. (Since we got the story through a mind meld in which the images and voice were dreamlike and surreal, it could be that the account was less than strictly accurate.)