Season three was like a haphazard dinner at a restaurant. You have a decent appetizer, then a scrumptious entrée, followed by an awful desert.

1 & 2. The Crystal Empire: Part one gave the season a great start. There were layers of great characterization amongst the Mane Six, notably Twilight Sparkle and Spike. The backstory of both King Sombra and the kingdom were also convincing, despite being brief. Its most notable drawbacks, however, were twofold (both in part 2):

• King Sombra's character was flatter than a board. What made Discord and Chrysalis engaging and more objectively menacing were how their personalities shone through. They had depth. Sombra was scary just for the sake of it.
  
• The plot crawled. Part 1 had an engaging plot that varied in pace. Part 2 had the pace crawl to a standstill as Twilight and Spike explored the Queen's castle while searching for the Crystal Heart.
  

Its strongest moment is easily the Door of Illusions/Door of Fear. It explored Twilight's greatest fear and desire to do whatever she can to pass the test. Twilight took this test so seriously and doesn't want to let herself, her friends, and Princess Celestia down. This powerful magic also gave Sombra the only layer given: his utmost cruelty for anyone aside his own.

While part one was great, part two was noticeably weaker. But it was still a hit.

3. Too Many Pinkie Pies: Dave Polsky's best episode by far. It was an episode full of comedy, but it also provided magnificent depth for Pinkie Pie, as well. Her clones were shallow and one-dimensional, with the minds of airheads, intentionally written to separate them from Pinkie's complex layer of care, laughter, and toughness. There was one obvious brony reference, too: G3!cloned Pinkie. The only flaw was the obvious Deus Ex Machina in the middle of Act 2 (where Spike discovered a secret cupboard within one of the back walls to reveal the book).

4. One Bad Apple: An episode that brought in a brand new eventual Cutie Mark Crusader: Babs Seed. The song is easily the catchiest of them all, with a great rhythm, great musical score, and psychedelic background. The CMC underwent the tortures of being bullied by someone who was coaxed under peer pressure to bully. The drawbacks in this episode were one objective, one personal:

• The revelation of Babs being bullied back in Manehattan came off as way too sudden. Even with the foreshadowing earlier in the episode, there was way too much buildup for the opposite. At least one extra hint while Babs joined the forces of Diamond Tiara and Silver Spoon would've given the twist a bit more convincing.
  
• Silver Spoon and Diamond Tiara were flat. In Ponyville Confidential, Diamond Tiara was given extra depth by being organized and conniving. She put the Cutie Mark Crusaders in hostage with the threat of having their private photos being released in order to embarrass the trio. Here, Diamond Tiara was a generic antagonist. The same can be siad for Silver Spoon, whom was given a little extra layer of depth in Family Appreciation Day when she was the first to applaud to Granny Smith. That layer was missing, and she was relegated to a sidekick again.
  

5. Magic Duel: Easily my most favorite episode in season three (and second-best in season three, too). My two analyses can be found here and here.

6. Sleepless in Ponyville: Magic Duel is my most favorite episode in season three, but this one is easily the best. I praised this episode here.

7. Wonderbolts Academy: At the time, it was the boldest episode with Rainbow Dash joining the likes of Snowflake/Horse Power, Thunderlane, Cloudchaser, Raindrops, and Lightning Dust (Dash's foil and episode antagonist). It was Merriweather Willimas's first Dash-centered episode since The Mysterious Mare-Do-Well (arguably the worst episode in the series and in season two), but she didn't disappoint here. WA is by far the best Dash episode since Sonic Rainboom (and easily Williams's best episode); her complex character was explored entirely, and she obviously learned her lessons from her previous appearances. Rather than finding a fault, her faults were showcased and balanced with her biggest strength: her loyalty to what is her family. Rainbow Dash's character is a concrete highlight this season after a disastrous first half of season two. I wrote the full analysis here.

8. Apple Family Reunion. Unlike the previous episodes, this one is akin to season one and two's slice-of-life episodes. It's tame, but extremely well-done. Applejack's previous episodes centered around her stubbornness and occasional drive to steer away from troubles. Here, she did whatever she could to make the reunion grand, only to have her plans fall apart so badly. It explores a really fantastic side of her: her dedication and love for her family. My most favorite moment of the episode was when Granny Smith said to Apple Bloom that not everyone may make the next reunion, leading up to Applejack's desire to make this reunion the best ever. Here's my full review.

9. Spike at Your Service: Here's where the season's quality began to objectively drop — It was a clunker that reversed Spike's progress in character throughout the series and season three. It had many good smaller moments (including some funny lines), but Spike was handled horribly through a very inane concept. Here's my full review.

10. Keep Calm and Flutter On: A complete reversal of SaYS. The previous episode had a great pace but a shoddy plot and characterization, but this one had easily the strongest characterization of the full cast and shoddy pacing. Fluttershy was extremely in character who didn't fall into being needlessly shy, She was strong-willed and did whatever she could to make Discord trust her in some way. Discord's plan to manipulate Fluttershy completely worked, but Fluttershy witnedd this plan from the very beginning and had him beat in his own game. She's tenaciously patient, and this episode showed the character development she received from Dragonshy, Putting Your Hoof Down, and Hurricane Fluttershy; she was given justice, and Polsky (and Teddy Antonio, the story's creator) deserve immense credit. But Discord's redemption isn't factually as convincing because:

• the pace was abnormally fast with no time to recuperate at any point.
  
• Celestia's throwaway line when describing her interest to have Discord redeemed was contrite and nonsensical.
  

It would've been a hell of a lot better if Discord's redemption was a two-parter; too much information was compacted into one twenty-minute episode, and the timeline was implausibly short. My full review is found here.

11. Just for Sidekicks: Easily my most hated episode of the season. Corey Powell is a wonderful writer who can handle the characters brilliantly. But Spike's character was written atrociously. Instead of being balanced with his greed and commitment to perform right, his qualities were sacrificed for his conniving and greedy sides, lessons that he learned in the past. Powell knows the universe, but tried to give Spike a flaw that he is capable of understanding the need to caution himself. There were several fantastic small moments, but Spike is the focus, so the episode is weighted by his performance. Spike's characterization was an absolute travesty, and I wouldn't EVER recommend this disgusting episode to ANYONE. Here's my full review.

12. Games Ponies Play: This episode I haven't watched yet. But that only determines whether I'll like the episode or not. But I read the transcript on the MLP:FIM wiki, and the characterization is bullshit. I'll skip it over.

13. Magical Mystery Cure: The songs are strong and progressed the plot. But that's really the lone strength (besides the animation; it's always been strong). The plot was way too fast, and Twilight's evolution to an alicorn had no momentum from TCEII onward. It was refreshingly dark in many aspects, but the plot whizzed through like flipping a storybook without reading the lines. Each sequences had no time to relax nor explore the consequences of the changing of the Mane Six's core. This episode easily should've been a two-parter to not just make the premise interesting, but also sell the Twilicorn concept better. The Twilicorn concept is factually stupid, and it was going to take something brilliant to make the idea convincing in the canon. (Liking a concept does NOT mean it's objectively a GOOD one.) M. A. Larson had to weave in the Twilicorn concept in the best fashion possible, and while it was a hell of a lot better than it could've been, but given Larson's intellect, it should've been much stronger. It had no momentum, and it showed through here. Overall, I'm okay with it, but objectively (sadly), this episode is a strikeout. The full review for it can be found here.

And she appeared at least five times, three of them WITH her derped eyes!

Overall, season three's episode quality is a mixed bag. There were so many great episodes in the first half, but of the last five episodes, only Keep Calm and Flutter On can be called good, and even that was greatly flawed. To put it bluntly, the biggest flaw in season three was its brevity. Seasons one and two progressed in several baby steps, but season three, due to its order of sixty-five episodes, attempted to perform bigger and more grandiose. Some episodes did a fantastic job (Wonderbolts Academy, Magic Duel), but it failed in others (Magical Mystery Cure). It felt like a final season in a series rather than a continuation for several seasons. So the team attempted to put forth more radical ideas that would make much more sense if given more time to foreshadow everything, especially the horrid Twilicorn concept. It forced itself to go bold, and it's evident by the really wavering quality of the episodes and even the ideas.

Nonetheless, I still have a lot of faith in the team. With season four having twenty-six episodes, there are many possibilities for the series to progress into deeper, more whimsical, and more thoughtful territories. I trust the writers and storyboard artists in getting the job done for season four. Who I have no faith in, however, is Hasbro: They're notorious for inserting some very stupid, series-altering ideas in the canon with no other reason than to sell toys. The results have been mixed, so I patiently wait for the subsequent quality of the upcoming episodes in season four.

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So, with that, here's my list of season three episodes (from most favorite to least favorite regardless of quality):

1. Magic Duel
   
2. Sleepless in Ponyville
   
3. Wonderbolts Academy
   
4. Apple Family Reunion
   
5. The Crystal Empire, Part 1
   
6. Keep Calm and Flutter On
   
7. Magical Mystery Cure
   
8. Too Many Pinkie Pies
   
9. One Bad Apple
   
10. The Crystal Empire, Part 2
    
11. Spike at Your Service
    
12. Just for Sidekicks
    

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Source: *SPOILERS* Season 3 Review Thread