Firmware updates fix some bugs and introduce others.

There are actually differences in the Prime and Kelvin timelines that happened before Nero's incursion. For instance, Kirk's date of birth is off by several months. They tried to justify that afterwards by saying something about the event sending shockwaves through time to change things before it even happened or something like that. The real reason probably lies in that interview where JJ Abrams admitted he never liked Star Trek, but you could argue that the removal of various down-stream time travel events, like the events of "The City on the Edge of Forever" likely not happening in the modified timeline, could actually cause retroactive changes to the timeline.

But anyway, the Kelvin timeline already diverges before the Kelvin-Narada thing, because reasons.

How did it take me until this comment to realize the name was a pun?

The wormhole / Celestial Temple seems to be extradimensional in some way. They might actually be out of Q's reach. Or they might not. Q's powers are vaguely defined.

I think the mushrooms almost feel too... mundane? The average person probably interacts with a lot more mushrooms than crystals. Crystals also have a long history of being associated with magical properties, and modern science has figured out some neat things that can be done with crystalline structures. We're pretty primed for crystals doing cool stuff. Mushrooms have significantly less mysticism associated with them and related science is more biological than technological. That's not really solidly in favor of one or the other, but it does mean the audience will more readily accept crystal hijinks with no warm up than mushroom hijinks with no warmup. The closest comparison to the mycelial network is Yggdrasil, which is solidly in the high fantasy category rather than sci-fi.

All that is to say, I think the mycelial network needed more time to set up than the show gave it. Some kind of foreshadowing, like simply mentioning something about advances in organic technology. Farscape probably would have been able to sell it pretty quick, but Farscape also has organic technology as a core part of the premise with Moya. Not an inherently bad concept, just kind of comes out of nowhere in the context of Trek.

Are thirteen year old boys not the target audience for the decon room scenes?

I didn't even get to listen to all of it because the app always wants to autoplay Hegemony.

The quote from Sputnik he read was especially memorable.

Sometimes you just decide to deal with that. I'm lactose intolerant, but I'll be dead in the ground before I stop eating cheese or ice cream. I just don't eat it frequently enough to be a continuous problem.

And just like Worf's backbone, it's dramatic when it breaks, but it'll be good as new by next episode.

I think they were banking on Vader hating the planet so much he'd never willingly return and then later training Luke in the hopes that Vader may hesitate to kill his own kids, because Vader hesitating to kill someone is basically the only way anyone has a hope of beating him.

If you think about it, logically, Tom is the original Riker and Will is the duplicate. Typically, the transporter moves mass from A to B, but can replace mass that's been lost along the way as a fail-safe. The missing original mass is either left at Point A or scattered along the transport path. The most likely thing that happened is that the transporter's fail-safe systems went overboard when they failed to pick up Riker's mass - rather than aborting transport as failed, it deemed it a successful transport with 100% missing mass and replaced every atom of Riker with spares on the transporter pad. Will is a transporter clone, Tom is the original.