Well, I watched Season 3 quite some time ago and never got through my thoughts on them.
The two Crystal Empire episodes were a little bit weak. I can't quite put my finger on it, but I guess I don't think there was really a strong driving narrative to it. Celestia saying Twilight wasn't to have the help of her friends was absolutely dreck, no matter if you believe she meant it or if it was a test to see if Twilight would disregard that and ask for help from her friends. The threat of Sombra was kind of in the background and he had only a couple of lines. Making him some sort of supervillain to be feared would have easily bumped up the show's rating, I guess, though the trap door showed some imagination on his part. Also, STAIRS! Bonus points for Spike saving the day for once and Shining Armor literally throwing his wife.
Too Many Pinkie Pies kind of ruins the Pinkie Pie mystique a bit, though Pinkie episodes tend to do that a lot. When Pinkie is in the background, she's the one that makes everyone happy, and the one with zany antics, but when you hone on her, she loses a lot of what makes her special as a member of the Mane 6 or cast in general. I do like the idea of the Mirror Pool, and the watching paint dry scene is full of great gags.
One Bad Apple has probably my favorite song of the season in 'Babs Seed'. Between the lyrics, upbeat instruments and actual visuals it just makes the episode perfect. The ending is a bit to Aesop-heavy but Babs is pretty chill and stuff.
Magic Duel. Trixie. Star Wars Homage. 'Nuff said. Simply awesome.
Sleepless in Ponyville I think I would put at the top of the season. Scootaloo finally gets her own episode, there's an enormous amount of character development on her part, some on Luna's, and we get Rainbow Dash wing-hugging Scoots. Rarity basically making Sweetie Belle do all the tough grunt labour of pulling her luggage is a fun running gag. It seems to me like as time goes on, the Cutie Mark Crusaders episode continue to get better and better, even as their overarching purpose of getting their Cutie Marks never comes to fruition.
Wonderbolts Academy is a strange episode. I like the general gist of it, and Lightning Dust makes a good foil for Rainbow. However, two things I think would made the episode better: make Rainbow even more cockier than normal to start the episode off, and be reckless like Lightning Dust is, only to change her mind and realise that she herself goes overboard with her attitude when she sees Lightning Dust endangering other ponies. Second, at the end of the episode, as far as it seems to be implied, Spitfire just demotes Lightning Dust without any warnings or anything beforehand - this, despite being the pony who made Lighting Dust lead pony in the first place because she was more daring, and even thought in the first place a tornado was a pretty chill idea, if a little overboard, when in a real-world command situation the commanding officer should acknowledge his or her fault in the situation as well. However, I now ship Thunderlane x Rarity based on the short scene of Thunderlane rescuing Rarity after taking the fall from the hot air balloon.
Apple Family Reunion gives us a very brief scene of baby Applejack and she is just SQUEE! It also sounds like just about any corporate family 'fun' party ever, though in this case for a big family rather than a company picnic. I'm always of the opinion we should get more Big Mac, and unfortunately he's still as in the background with very few speaking lines as always, getting little more than a gag on sneaking an apple fritter.
Spike at Your Service. YUCK! Spike's been shown to be rather useful help in previous episodes, which includes cooking and cleaning, and then they decide to throw that out the window completely and make him some sort of dumb klutz. OH SPIKE BURNED THE PIE! ARE YOU LAUGHING YET?! It makes this episode worse that all they really had to do was simply not make him a klutz, and turn it from an 'Applejack doesn't want to hurt his feelings' plotline into something slightly more ethically charged, 'Applejack finds his help useful but wants him to be able to have his own life' instead. That, and get rid of the scene at the end where he beats a Timberwolf by throwing a pebble at it. That was stupid.
Keep Calm and Flutter On. Discord is an epic troll and practically steals the show every scene he's in. I think this should have been a two-parter, if only because a single episode isn't really enough time to make the whole reformation believable. Also holy smokes did Twilight Sparkle actually yell at Princess Celestia for once?!
Just for Sidekicks and Games Ponies Play tell the opposite stories of the same day. I can't quite say I enjoyed either of them, though Games Ponies Play does lead into a storyline that occupies several episodes of the next season as well. Just for Sidekicks runs with the whole 'make Spike dumb and immature all the time' plot too much. Spike's a kid, so I would expect him to make mistakes all the time and sometimes not owe up to them, but episodes with him seem to always go to the extreme. Games Ponies Play, seems to me that for all they keep making Twilight a Canon Sue that you would think she would make sure the pony they picked up was Ms. Harshwinny. However, they're already getting rid of the one thing that really made her interesting by having her go through breathing exercises every time she gets close to panicking.
And finally, Magical Mystery Cure. I wasn't a fan or anything and I only ever watched the first half of season 1, so I wasn't around for the whole blowup this episode caused. In theory, I don't really have a problem with them making Twilight a Princess, or giving her wings. I mean, she's been pretty much a Canon Sue since close to Day 1, outside of her neurosis, which Games Ponies Play showed was getting better. What I _DO_ have an issue with is the trigger for her being made a Princess and Alicorn. at least when you compare it to Star Swirl himself.
Let's see. Star Swirl the Bearded? Created more than two HUNDRED spells according to Twilight in Luna Eclipsed. Presumably created the Time Travel spell from It's About Time, since it's in a library wing named after him, though somepony else may have created it. As we learn in Season 4, befriended a supervillain and turned him against an unrepentant supervillain. Started but never completed the spell at the heart of MMC. Not a Prince, not an alicorn.
Twilight Sparkle? Element of Magic, she does save Equestria twice, but she only is ever shown to merely COMPLETE a single spell, and convinces her friends of their true talents again. For this, she becomes an Alicorn Princess. If she had defeated Tirek as a unicorn at the end of Season 4, then I could have bought that being the reason for her being made into a Princess, but this just seems a bit too early on.
Also, the other thing I don't like about MMC? It makes it look like Ponyville would fall apart if the remaining five of the Mane 6 weren't performing their true talents. That's pretty much making everypony else useless.