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> The zipline opening is funny and a quintessential CMC trademark of ill-advized antics, enjoyable to see as always! Scootaloo also mentions that Spike told her that ziplining is awesome, and I could definitely see Canterlot having ziplining.
Now that you mention it, that makes sense.  You have this city on terraces attached to the side of a mountain, and most of its residents cannot fly.  They have balloons for traveling upward and presumably downward, but ziplines would be a faster and more practical method of traveling downward.  From there, it would stand to reason that Spike would know quite a bit about them despite being a toddler.
> Fluttershy in her flashback appears to be older than Applejack was in hers, and that’s where we start to get the whole comparative age debate with the Mane 6 – although most of the others seem around the same age so perhaps Fluttershy is just lanky or got an early growth spurt.
See: above.  We know that Fluttersy is a year older than Pinkie Pie, and that is the only thing that we know about them age-wise from the show itself and not the word of Faust.  Even there, we do not know if that is a human year or a horse year, which is rather significant for fillies in terms of development. Another possible reason for Little Fluttershy's unusual size is that Faust had originally wanted the ponies to have different body types but the idea got scrapped due to budget constraints  Thus Little Fluttershy's height was a call-back to that early concept.  I have heard it mentioned (can't recall where) that Rainbow Dash was originally supposed to be very short.
> When her horn starts acting on it’s own, Rarity mentions how unicorn magic doesn’t happen without a reason and connects it to her destiny when it brings her to a boulder, suggesting an interconnection between magical talent and cutie marks within unicorns.
"Dumb rock" began Rarity's rocky romantic relationship with large mineral deposits.  I love it just for that.
> In Twilight’s flashback, we learn of her eagerness to see Princess Celestia to raise the sun, and how this inspired her to pursue magic for herself, which I think goes some way to explaining Twilight’s sometimes quite extreme loyalty and devotion to Celestia, as well as the neuroses that sometimes crop up from that as a result.
It is notable that this is a wildly different origin story than Twilight Twinkle's which involved a late-night study session after she had already become Celestia's student.
> The Sonic Rainboom has some rather odd and mysterious properties and I don’t feel like we actually know all that much about it (it’s referred to as an ‘old mare’s tale’ after all), but I still feel it would be a stretch to say it can actually imbue a previously weaker unicorn with some of the strongest powers that we regularly get to see in the show, even IF that’s the interpretation that was in mind when the scene was made. So long as that connection isn’t explicit, I’m happy going with more or less any alternative.
I honestly do not know why they went with the Sonic Rainboom for Rainbow Dash's cutie mark story.  It does give the six main characters a connection, but was that even necessary?  I greatly prefer the original concept where Rainbow Dash flies fast enough to create a vapor trail that causes a rainbow to appear.  The idea was that pegasus ponies gathered bunches of clouds to create rainbows that would then serve as solid bridges, which is why Cloudsdale looks the way it does.  Apart from just shamelessly ripping off Olympus from Disney's Hercules, that is.