I'd say quite the opposite as to me was a take on prejudice and it handled it quite well as it not only didn't paint the ponies as being wrong for holding their beliefs towards the changeling which who can blame them as I'll get to below, but also showed of how not every person from the opposing side is a bad person and that some are capable of changing for the better.
It was with the help of Spike that:
A. Saved Twilight Sparkle who was going to fail miserably when a trap sprung on her when he disobeyed her to not follow her to find the crystal heart.
B. Whisked the Crystal Heart away from the pedestal when again Twilight was ensnared in a trap and Sombra was closing in. While Cadance deserved credit too for saving Spike from Sombra's clutches but Spike should earn kudos for getting Twilight to that spot and recovering the crystal heart for her.
C. Helped save the equestrian olympics from a disaster by melting the ice.
Considering all of these at least it would make sense for why the Crystal Empire would view him so favorably, especially as he's treated with great respect by the royal family for his deeds.
As for why he and not the mane 6 get kudos for their efforts, it is because of:
A. The show runs on the trope that the mane 6's deeds in saving equestria aren't mentioned for the sake of not paying such attention to it.
B. For Spike's case however they have chosen to to give Spike some respect to his character.
C. The Crystal Empire is not like the rest of Equestria as they have their own customs and what not, so they chose to worship Spike for saving their kingdom from Sombra and the giant ice at the equestria games.
D. Spike himself loves it as it helps boost his own self importance so I don't see any problems with it.
The thing is is that Spike is risking his reputation that he has built up and earned with the crystal ponies and especially among the Crystal royal family as especially Shining Armor have shown to despise changelings so him showing support for Thorax puts his butt on the fire to where he could lose a great deal of respect among them for supporting a changeling as he would be viewed as foolish at best, traitorous at worse. I mean folks have lost their reputations for far lesser crap, him supporting a being from a mortal enemies to ponies would be the ticket for it.
It's a little thing that Cadance and Twilight would know how to do between each other and it's a cute callback from past seasons of their little dance number they had between each other. I see no issues for it. As for why they assume that Starlight and Spike are fine, they're newcomers that just arrived alongside Twilight and they assume that if Twilight was able to vouch for them and she was real than it was fine. Not everything needs to be tight and close to be 100% certain that they're changelings, especially as they said that the changeling was spotted in the crystal empire so I wouldn't expect newcomers like Twilight and her companions among the chief suspects.
As for the stuff, you're assuming that Spike is going to think of the situation similarly to how you would approach it. He was convinced that Thorax was honest with his story, and especially as he saved Spike from falling to his death.
As for the others, they were paranoid and didn't trust Thorax as it took essentially Spike putting his reputation and vouching for him on the line to show how much he trusts Thorax and wishes for others to do as well and an alicorn princess in Twilight to further recommend they do the same. Again they're not going to approach a situation similarly as what you believe they should but instead should see if they're approaching a situation with justifiable cause and action which I believe they have.
Because you're assuming that Thorax could pull it off well as we see that despite his disguise, due to his hunger, he'll lose it and expose himself which was likely how they found out there was a changeling in the first place. Spike's plan is not stellar but given the circumstances and what he could do it was literally the best plan Spike can do for Thorax as they try to figure out what to do to get him to feed in a manner that wasn't going to hurt anyone as Thorax feared doing.
You can blame it on the lax security for not checking identification for him at the gate or so true however. Though I do not consider it such a flaw as they did do security sweeps and stuffs just not to the extent one should expect they should do.
I think this point here is a case of one thinking deeply for larger contexts of those scenes rather than something inherently wrong.
Actually it's pretty justifiable for Shining Armor to behave like that to Changelings considering how:
A. Queen Chrysalis kidnapped his wife and guised as her.
B. Brainwashed him and drained his love for her own needs. Which leaves far darker contexts between Queen Chrysalis and Shining Armor in that case if we're to assume they slept with each other.
C. Used his love to defeat Celestia and nearly take over Canterlot and threaten Equestria with her changeling army
Thus in the show alone, he had justifiable reasons to hate the changelings as much as he did. Hell I loved that as it showed good characterization on his part, something I wish his wife was a little more consistent in that regard.
This is not including the comics to where we see
This
And
this
Where Queen Chrysalis and the changeling horde wrecked at least two Equestrian cities and they gotten so bad that Celestia herself in her youth went and stopped them personally and threw them inside a volcano.
Lorewise, Changelings are the Equestrians biggest enemy in existence as the changelings seem to be predators to the Equestrian pony prey. So put all that together, it makes total sense for any pony to behave as Shining Armor did.
While it's true that Thorax was different rather than change for them, however in context this can open up to where we see more friendly changelings as it's shown that there are friendly changelings out there and while Thorax has a long upstanding battle against Chrysalis and the rest of her changelings, however considering what they have done with Gilda representing Griffons, the Yaks, and Ember for the Dragons, I assume they have a plan waiting in store for them and intention for what they could have in store. Who knows, perhaps he can help bring about the change they need away from Chrysalis's war mongering rule.
Yes considering how Twilight and her friends did friendship reports so it makes sense for Starlight to be taught in a similar manner. Heck there's an upcoming episode this season that will explain more on it.
I'm sure it's something he agreed to do considering that he holds a prestigious position of not only taking care of the crystal but also being a royal nanny has it's perks for his reputation so I'd say he's in a happy position in his life. Much more than his life as a bitter librarian and scholar.
I think this point is thinking a little much on how Spike is able to convince coming and going as he pleases, especially with his reputation and such in the empire.
The reflection gag is actually based on an old time joke here:
So it was meant to be funny rather than being anything super serious.
As for showing off the baby, here's why:
But other than that, I'm sure it was so he can feed safely or something like that he was still starving so I'm assuming this was them allowing him to feed off from the love the baby had. For other ponies, they're just proud parents to say the least.
Thank you very much, music chart fan.