Note: Expanded my original thoughts. Credit also goes to @AlexanderThrond, @Odyssey, and @OptimisticNeighsayer for it.

With a world as magical and fantastical as Equestria, any form of mystical being is possible. They may sound like fairytales (or "pony's tales," as what Spike once said about the Mare in the Moon). Not too often does the show do the opposite: establish the legend of a mystical jokester no one witnessed and make both ponies and viewers wonder if he doesn't exist. Considering the amount of lore in the series (both in the TV series and comics), it's an undertaking for the show to give this concept any benefit of the doubt. That was partially Applejack's role, as her stubbornness and eye for logic initially play a role in downplaying and explaining other ways for phenomenons to work beyond a "just-because" shortcut.

Additionally, Applejack's stubbornness usually lasts all the way through the climax. The Mane Attraction is the lone time to use it as a strength rather than a flaw. Just like the lore, Rapp reigns her flaw in. Instead of making her impose her stubbornness on everyone else, she's stuck with a dilemma: promise Granny and Big Mac to help round up every apple in Sweet Apple Acres and not try to hurt Apple Bloom's feelings. More on this later.

Building up this dilemma in the first half was its biggest weakness, and there are a few reasons why.

1. The first half is loaded with exposition. The rest of the Mane 8 were written off early, automatically turning it Apple-focused. But using a one-line shortcut cheapens the direction. Even the lore of the confluence (the time where every apple is ripe simultaneously) doesn't hold much weight, as it's attached to the clunky "moon" length of time and explained very early on. Additionally, the episode repetitiously reminds the viewer how catching the Sass Squatch-like trickster*; once is fine, thank you.
   
   *The AJ Micro revolved around a "Sass Squatch," a mystical creature that changed apples into squashes, and Applejack was stubborn as Boulder to try to capture him alone for most of the issue.
2. Until the end of the flashback, it was really slow and bland, with surface jokes that aren't all that funny. Usually, they were related to either Goldie's "crazy-cat-lady" shenanigans or Big Mac's exhaustion, and nothing more beyond that. One of the only ones to work that well was Goldie's cats distracting her to steal her pancakes.
3. Although it was a problem for the whole episode, the dialogue in the first half was quite repetitive. I don't need to specifically hear "Great Seedlin'" all the time.
4. Throughout most of her time as a foal and filly, Applejack learned of his legend and the reward for catching it, so he spent good time every confluence to set up traps rather than buck the apple trees. However, she forgot where one of the traps were and was stuck in a deep hole for most of the day. She felt so upset for it that she felt like she let herself and her family down over trying to chase a mystical creature that may not even exist. Therefore, as what @OptimisticNeighsayer wrote, she established a "sour grapes" approach to the fairytale, eschewed the Great Seedling as nothing more than fairytale, and focused primarily on working the farm. It established why she can be so work-driven (nicely pointed by Alexander Thrond, his post linked further down), shown in past episodes like Applebuck Season and AJ's "Day" Off.
   
   So why is this, by far, the worst moment of the first half? Because of this:

   Quote

   Granny Smith: [voiceover] She spent the better half of the day stuck in that trap! [laughs]

   Applejack: [voiceover] And missed out on helpin' with the harvest because I was chasin' somethin' for little foals. I felt guilty everypony else had to work harder because of me. So I decided right then and there I was too old to waste any more time on Great Seedlin'.

   Granny Smith: Oh, we finished the harvest just fine. But we laughed about that story for years! [laughs]

   Goldie Delicious: [laughs] I'm still laughin'!

   Goldie and Granny don't treat her mistake as a big deal, even though it is to her, evident by her tone and glum expressions. Combine that with Goldie's smugness, Granny's decision to explain right there why AJ became cynical in the first place, and their disagreement from earlier, it unfortunately implicates that Granny told AB the story as a "gotcha!" to put AJ in her place. AB tries to soften the blow by staying by her older sister and refusing to join her grandma and relative (and Goldie shaking her hoof after they accidentally ran too close was a little bit of accidental karma), but neither of them were held accountable for not taking AJ's hurt seriously, making the overall tone of the moment and flashback really mean-spirited. To borrow from @Odyssey, if it wasn't shown in AJ's point of view or have her bitterness dominate the mood, then perhaps the scene would feel more whimsical, and the tone's direction wouldn't be so convoluted.

Thankfully, the rest of the episode picks up from there, focusing on Apple Bloom and AJ's bond. Whereas Sweetie Belle and Scootaloo had bonding episodes with their older sisters (both biological and surrogate) previously, AB never had that, as episodes where she shares a focus are more on herself (and for Brotherhoves Social, her relationship with Big Mac). The one time where there was some kind of bonding episode between her and AJ was Somepony to Watch Over Me, and that's an AJ-focused episode and AJ's worst appearance of the first five seasons.

Recall AJ's dilemma that I mentioned earlier, and I'm going to expand from @AlexanderThrond post with my own thoughts. Yes, she wants to help everyone else, but catchin' him mattered to AB. That's why she was gentle when talking to her about it and tried to add uncertainty to the legend. More importantly, AJ didn't want her own trauma to similarly affect her. In short, to softly ask that question of the Great Seedlin' being real or not was a warning without trying to intrude. But she was also willing to help her and make her happy however possible, which is why they agreed to compromise on Day 2: If they work together to harvest the trees, they'll set up the traps later. Rather than make AJ so stubborn to the point of blindness like her Micro, the episode eases her stubbornness and allows her to be open-minded to his existence being possible. This moment and AJ's flashback tie a little bow on the first half and commence the second half's direction, giving them the bonding episode they sorely needed. Two moments, though, really stand out.

1. Their montage was really heartwarming. Rather than let Granny and Goldie get the best of her, she helped AB prepare the traps, using both her own memories back in the day to place them in the best spots and ability to build to build them faster and effectively. Skeptical at first, she progressively showed to having a lot of fun setting them all up. Pay attention to the change of facial expression from this to this to this. When she said she had fun, she meant it; the facial expressions and length of time they put in to building those traps back her up. You can tell she was starting to evolve from an ol' prune to a shiny plum. This was the first confluence since she was a filly, and by helping AB, she reminded herself of the good fun she had then. Yes, she still has responsibilities, but quality time with her young sis healed painful wounds and let her loosen up in life.
2. While Big Mac struggles to clean the orchard on time, AJ and AB are having fun off-screen, and after discovering an empty orchard, they'll accept any help possible to solve it, including listening to one of Goldie's Great Seedling tales. After some advice on how to improve their chances of catching him, they have one of their best heart-to-heart moments of the series.

   Quote

   Applejack: I couldn't have been much more than a foal. I remember our parents tuckin' Big Mac and me in and tellin' us all about the Great Seedlin'. And I got so excited, I could barely sleep. So I—

   Apple Bloom: [snoring]

   

   Applejack: Don't you worry, sugarcube. I won't let him get away.

   

Now, even though they don't know Big Mac unintentionally disguised himself as the mythical deer, the episode makes his identity way too obvious. From the opening shot, the camera spies on him being exhausted at the table and accidentally falling asleep on the breakfast table. Over the next eighteen minutes or so, his expression and behavior deteriorate, such as sleeping on the floor, not observing his surroundings, sagging and drying eyes, not cleaning up the apples right away to knock the apples down easier, sleepwalking, and so on.

However, despite the mystery behind the Seedling, that wasn't the point. Its focus was on Applejack eventually letting her hair down to reminisce and enjoy being a kid with a sister who was too young to participate last time. The hunt was merely the plot device to bring them together.

So is it the worst episode of the season so far? Yes. But compared to the previous first halves, is this way better than Boast Busters, AJ's "Day" Off, Fake It, and The Cutie Pox? One hundred percent. Overcoming first-half hiccups, Going to Seed's the AJ Micro done better and a fine overall addition to the series.