That's exactly the illusion people keep falling for. Memory is unreliable, because we gloss over the rough bits to smooth things out. We convince ourselves that older Trek was more consistent than it actually was, because we get in the habit of rationalizing or excusing its contradictions and learning to think of them as "minor." So the new ones always seem huger to us.
And even if some of the changes are bigger, so what? It's fiction. It's an invention for the benefit of an audience. An audience today is going to be massively different from an audience 50 years ago or 30 years ago, so naturally the differences in the presentation of the fiction are going to be proportionally greater to keep up with the audience's evolution. It's all just stories. You can change the story as you go, improve the way you tell it.
It doesn't have to be reconciled. The Klingon foreheads didn't have to be reconciled. Roddenberry's view was that Klingons had always had ridges. The change wasn't an event within the story (diegetic), it was a revision in how the story was told (extradiegetic).
Of course, SNW already offered a diegetic explanation for the changed depiction of the Eugenics Wars in "Tomorrow and Tomorrow and Tomorrow," establishing that 20th- and early 21st-century history have been altered by temporal interventionists in order to explain why we didn't have Eugenics Wars in the 1990s or the Millennium Gate in 2000 or whatever. Although the premise is that counter-interventionists or the inertia of the timeline caused things to converge back on their original path by the 22nd or 23rd century, so that events are still pretty much the same then, down to details like Pike being fleet captain when Kirk met him. But yeah, if you like, you can use that as a handwave for the superficial differences in set design and whatnot.
The explicit job of tie-ins, the reason they're called that, is to follow the lead of the onscreen franchise. If the onscreen franchise purports that all Trek series are a single reality -- which is exactly what it does purport despite any changes in how it presents that reality -- then our job as novelists is to depict it that way. That has nothing to do with the standalone vs. serial difference you mention, because that's a matter of whether the novels agree with each other. All novels are obliged to agree with the onscreen canon as it exists at the time of their writing, regardless of whether they're consistent with one another or not.
I'll never understand people who only want fiction to remind them of what they already think and know, rather than offering them new possibilities and new understandings. I mean, that's the whole purpose of art.
I hate everything SNW has done with the Gorn. But that doesn't make SNW an alternate reality from the rest. There's plenty of stuff in the older series that I didn't like. This is the nostalgia illusion -- people choose to focus on the good parts of the past and not think much about the parts they disliked, so they fool themselves into believing that the past was better than the present. They forget that every Trek series had its bad parts and its dumb parts and its inconsistent parts. We didn't like it because it was perfect, we liked it because the good parts were good enough that we were willing to live with the bad parts and the middling parts. As long as I remember that, I'm able to judge the newer shows in the same way.
