Note: Credit to @Ganondox and Loganberry for this review.

Like using Chrysalis to explain past events to the Everfree trees, much of what Vogel uses to start What Lies Beneath is exposition to describe the Tree of Harmony, its history, and purposes. But rather than using a character babble it out, it's told in the context of a classroom lecture followed by studying for a surprise test, and it wasn't all explained immediately or through one mouth. When Twilight lectured, students either asked questions, didn't believe her, or became frustrated over not knowing pony history, organically informing the audience of its lore.

Now, whereas HW Club gave the Young Six the boost they truly deserve, WLB expands them further. Each of the Young Six start having doubts over whether becoming friends with others is natural to their consciences, culture, and themselves. Cozy Glow nicely sets up the conflict by going deep into parts of the Young Six's psyche, exploiting areas of their culture and livelihoods that are really sensitive to them. Is it racist? Absolutely; she's stereotyping the creatures as inferior to ponykind, and given how dubious she's been this season, it's intentional. Unlike Neighsay (whose racism is mixed with bitterness), her manipulation is masked with sweet innocence and then changes the subject, as if she meant no harm. Yet, pay attention to the moment afterwards and their little argument that night in the library, started by Gallus after getting annoyed at Silverstream for tapping her claws on the table. Her superiority complex cut deeply in them.

And it's at this moment where the episode turns into an improvement of two past episodes: the pilot and The Crystal Empire. To get this out of the way, I agree with both Loganberry and @Ganondox regarding the Tree of Harmony's tests for the Young Six. Not only were they really harsh, but also morally questionable. What if Gallus failed his test? Would he be trapped in the enclosing cavern forever? Would the Tree create another test? Or what about Yona's arachnophobia; will she become so scared of spiders that she'd rather kill them over acquainting them? Fear is reactionary and not always based on logic.

(And the dialogue was also a little rough with plenty of repetitive dialogue.)

So, why does the Tree get a pass when Celestia and Luna don't?

1. The Tree is omnipotent and understands the characters' strengths, weaknesses, and virtues. After seeing a friendship-related problem, she ties it to being(s) who can successfully heal it. Sometimes it's one, two, or more, depending on who and what they all have in common. Of course, this is a little different, because she tests them to determine whether they can become friends with each other or not.
   
   Additionally, despite its strong powers and subsequent growth, it can't fix it alone. Faith is placed upon them, and it's up to them to use their knowledge and friendship capabilities to solve it. OTOH, Celestia and Luna already defeated King Sombra, who cursed the Crystal Empire into disappearance. But after one of their guards alert of their resurgence, what does Celly do? Write to Twilight and place thousands of lives on her shoulders! Conversely, the stakes here are nowhere nearly as severe.
2. In addition to needlessly putting countless lives on the line, they assigned her and her friends to take part in Twilight's challenge, but Celestia warned her that she and only she can save the Empire, contradicting the assignment Celestia placed on her since the beginning of the series. If she goes against the test in any way, she risks failing. So once she's trapped and requests Spike to return the Crystal Heart to its altar, she's rightfully worried, hence her dismay after Sombra's defeat. And the episode also has the gall to emphasize passing the test as the most important plot point over protecting the empire from Sombra, which makes the sacrifice lesson she spewed really hypocritical and phony.
   
   WLB counteracts this. Firstly, the Tree can't mandate them to take her test; they choose to explore what was under the drain grate she popped open. When Gallus crossly questioned her tactics, she was precise in her reply. Secondly, from the start, she explicitly tested their meddle to make them prove whether friendship's in their nature or not. She has the wherewithal to know that, yes, they'll break free, but will also not leave until they found each other. Tightening their friendship was the purpose for her tests, and the moral excellently backs her up.

And how does WLB improve the pilot, specifically Part 2?

1. Vogel spends a great deal of time equally pacing and exploring each of their fears along with sensible ways to face and beat them. Gallus and Smolder beat theirs first, but WLB doesn't forget about them. Instead, when one of their friends is very vulnerable and doubts if they'll ever conquer their fears, they bond with them more and use their own experiences as an example of overcoming them. The bonding between Ocellus and Smolder has added weight, because changelings and dragons retain an awful reputation (dragons for their brutish nature and history of terrorizing pony villages, changelings for nearly overthrowing Equestrian royalty twice), and the same can be said with Silverstream's horrific belief that the Storm King will reconquer Mount Aris.
   
   One little thing that gets overlooked is what Smolder and Gallus say after they arrive at the cave entrance…

   Quote

   Gallus: Maybe the others got out already and we're the last ones?
   Smolder: [sarcastic] Yeah, that totally seems like something they would do.
   Gallus: [groans] Any other dragon or griffon would save themselves and get out of this crazy cave.
   Smolder: Guess we aren't just any dragon or griffon anymore.
   Gallus: Guess not. You go that way. I'll check over there.

   …AND after reuniting with all but Sandbar:

   Quote

   Gallus: The way out is closing! Smolder: We aren't leaving without them!

   Yona: Yona realize no reason to be afraid. Spiders and yak friends! So Yona ask new friends to help finding old friends!
   Gallus: Do you think your new friends can help us find Sandbar?
   Spindle: [chitters, leads spiders away]
   Smolder: Of all the strange things that have happened tonight, that's the strangest, right? [Everyone follows]

   With every opportunity to leave the cave, they willingly risked being trapped to find the others. Twice. No matter the consequences, they were NOT leaving ANYONE behind! Their friends matter, period!
2. When the Mane Six were tested in the Everfree Forest, each one was segmented. When one trial ended, another began, and they were all written in to prove they properly represented the Bearers of Harmony. Sure, individualizing them isn't a bad thing, but by splitting them all up into only a few minutes, none of them had time to develop or breathe. Each segment was crammed, and be being bound to the E/I rating, the stakes weren't heightened as much as they should or paced more evenly.
   
   By contrast, Vogel intertwined each and every one of them simultaneously. None of their tasks ended at once, but he neither rushed them through nor ended them abruptly. He gradually built up their fears, exploited them, and ended them properly. What do I mean? They conquered their fears at the right time of the story, used the right characters to help pass their tests, and only after Vogel exhausted development of those fears.
   
   No matter the tone, each of their fears are treated with equal validity: Smolder's fear of femininity overtaking her persona was by far the most lighthearted, but the episode didn't treat it as a joke and utilized it as an example of being able to change from who she once was to Ocellus, who recalled how they used to treat others back then. The Storm King was already destroyed, but Silverstream's fear of his return resulted in her cheerful, optimistic personality being replaced to debilitating fright to the point of crying. Gallus realized his "return" was a mirage, but that wasn't enough for her. So he used his fear of small spaces, helped her overcome her fear of his return, and she let it all out to him.
   
   How Yona faced her fear was the most different. Gallus's trick foreshadowed what was to come, but when spiders faced her, her strongman personality gave way to intense arachnophobia. When spiders got too close, she was justifiably upset. With no friend she knew around, she wished they were there so she could get out. But in a twist, the lead spider Spindle talked to her. What the spiders were doing was that they weren't trying to scare her. They wanted to help, Spindle leading by example. Language barrier aside, they shared something in common: befriending each other and reuniting her with the others.
   
   Recall the second quote box above. Sandbar's fear's more subdued, but nonetheless validated. From the beginning, he focused on returning to his friends so they, "Dash," and "Rarity" can go on this adventure. Every time he questions his teachers' logic, they manipulate him into removing doubt and forcing him to run in a massive loop. Soon, he has enough, questions them outright, and when they express disappointment in him for caring about his friends than them, he turns the tables on them. As he lectures them, his friends arrive and watch from behind, adding more weight into how much they mean to him. He may be the quietest and most straight-man-ish of the Young Six, but he also needs to grow; confronting his fear of disappointment head-on was a fantastic solution.
   
   Without the constrictive E/I rating and by rearranging the plot, Vogel legitimized the stakes without phoning them in, which makes us invested in their obstacles, friendships, and outcomes.

This next paragraph deals with spoilers for the S8 finale and S9 leaks/speculation, so it's under the tag.

Overall, What Lies Beneath is another really excellent episode within S8B's fantastic lineup.