My six cents (adjusted for inflation):
- Sleepless in Ponyville (D'awwww! Excellent dream sequences, plus Luna!)
- Wonderbolts Academy (Rainbow Dash doing the right thing, even if it means giving up her dream)
- The Crystal Empire, Part 1 (Helping the Crystal Ponies remember who they are, plus Celestia can be scary!)
- Too Many Pinkie Pies (FUN! FUN! FUN!)
- Keep Calm and Flutter On (Fluttershy breaks Discord - well done!)
- Magic Duel (Trixie's corruption and subsequent redemption)
- Apple Family Reunion (AJ's OCD episode - not bad)
- One Bad Apple (Not a big fan of the CMC)
- Just for Sidekicks (A little too much focus on Spike's greed - we already saw that in "Secret of my Excess")
- The Crystal Empire, Part 2 (Weakest villain to date - they could have done so much more with him)
- Magical Mystery Cure (What the hell just happened?)
- Games Ponies Play (They REALLY tried too hard with this one, IMO)
- Spike at Your Service (Same here - Spike is noble but almost completely inept! Seemed very inconsistent.)
I think overall this season had some very good stuff in it, but like Kyronea, I feel it had a lot of missed opportunities. Sleepless in Ponyville is now my top favorite episode of the series as a whole, and other notable moments in Wonderbolts Academy, Too Many Pinkie Pies and Keep Calm and Flutter On made this season memorable. But I also felt that this season had the lowest lows of the series as well - I really didn't like the finale nearly as much as those of the first two seasons, and it felt like as the season neared its end, the plots were starting to get into shark-jump territory. I feel like the show was trying too hard to maintain its velocity.
Now, to be fair, I totally understand how difficult it can be to maintain the velocity that it had established in two full seasons of excellence. While neither Season 1 nor 2 were perfect by any stretch, they must have done SOMETHING right to have gained such a following. But I mentioned this last week that keeping all the characters "status quo" would inherently limit what the show could do, and would put it at risk of jumping the shark just for the sake of keeping it interesting. I think Season 3 came perliously close to doing exactly that.
Now that Twilight is an Alicorn and a princess (of what, we don't know yet), the show has room to expand into new territory and explore different aspects of friendship that were simply unavailable before, and I have faith that they can do it without grasping at straws or flying over hypothetical large fish. I think the show would have stagnated if this hadn't happened. I just wish the ascension had been executed better.
I kinda wish one of the Studio B staff would explain why the finale was so jam-packed. I strongly suspect that Season 4 hadn't been announced until the finale episode was already being produced (or might have even been finished) - it would just be cool to find out if that was indeed the case. I suppose I could forgive it feeling like a series finale as opposed to just a season finale if that's what happened.