After the kind of "meh" season 3 (which still had a couple strong episodes), I think season 4 made an overall nice recovery and stand with seasons 1 and 2 fairly well quality wise. I've been watching the episodes as they've been released since early 2011, so I started with the show towards the beginning of season one. The show has changed since then, not in catastrophic ways, but in some ways worse, and in others better, overall, I'm still interested enough that I am awaiting season 5 with some excitement and optimism, especially with the return of M.A. Larson as a writer and Thiessen as a director.
For me, I rank the seasons like this:
Season 2 is probably still my favorite overall, with both a really strong open and close with 2 of the series best villains in Discord and Chrysalis, combined with a pretty solid quality all throughout with the slice of life episodes. The season struck a good balance between developing the world and setting building, and character interaction with episodes like Nightmare night and Hearth's warming helping to flesh out the society and history of Equestria, while other episodes gave us interesting interpretations of mythological creatures, with characters like Iron Will, Ahuizotl, and cerberus. The character episodes also expanded the CMC beyond mindless one trick characters and gave them meaningful interactions with their family and each other.
The season also ditched the obsession season 1 had with cramming Twilight into every single epsiode so she can write the obligatory morality letter. The expansion of the letter writing was also a nice touch, and allowed the episodes to focus entirely on the other 5 ponies without always using Twilight as a framing device. This season also has 2 of my top 5 songs in the series in the Smile song, and This Day Aria respectively.
Season 4 just beats out season 1 for the number 2 spot in my book. The season opener was weaker than season 2's, but it was solid, and didn't feel nearly as cheesy as season 3's opener, or as rushed as the pilot episode. The slice of life episodes were overall pretty good, and the return of the morality mechanic in the journals was a nice touch, even if I still liked the letters just a little bit more. There were a couple duds, but every season has those, and the overall quality was good for me.
The overarching plot with the keys was also a nice framing mechanic, and gave all 6 of the ponies a specific episode for them to shine in. Some of the key episodes worked better than others, but I think it did a good job of breaking up the monotony of solid slice of life episodes between the 2parters at the beginning and end.
The characterization of Twilight and Discord was actually pretty top notch all season, and almost seemed specifically set up to answer questions after the rush job that was Discord's reform and Twilight's coronation in season 3. With Discord, they did a good job at showing that the lesson he learned in season 3 wasn't really something that changed him, and he was still basically a slightly more restrained antagonist all the way until the season 4 finale where the consequences of his flippant attitude finally bite him back and force him into an actual bout of self-reflection that makes his gradual reformation much more believable. With Twilight, while the princess thing was ignored at odd moments, and the Twilight Time episode was kind of strange with only kids seeming to care about her status, she has a good season character arc where episodes that focus on her tend to have her expressing doubt or uncertainty over her position, culminating in the fears expressed in the finale.
Overall, the season capped off with a good finale that has a good villain with Tirek who is worthy of being compared to Discord and Chrysalis in the previous seasons. The finale tied everything together pretty well, and the proclamation by Twilight that her duty is to spread friendship across the land gets me excited that next season will see more locations outside the usual Ponyville, Canterlot, and crystal empire settings. The rainbow power design is silly looking, so I'm glad that's only temporary, and the Twilight castle isn't bad, but I'm hoping it gets decorated to fit more with ponyville's architecture, rather than looking like something out of the crystal empire. The touch with all the ponies (and Spike too) getting thrones in the castle, and having them set up like the Round Table from king Arthur was a very nice touch, and I want to see them do something with the setup next season.
For me, Season 1 is great, and still has some of my favorite episodes, but it's got kind of a weak opener, with Nightmare Moon being kind of a cliche kid's show bad guy who didn't have nearly enough presence compared to Discord, Chrysalis, and Tirek, although she still beats the pants off Sombra. The midseason episodes were what got me to give the show a chance so I mostly like them, the morality lessons were mostly obvious, but they provided a good framing device for some of the episode plots, and characters like Gilda and the Diamond Dogs are still classic character designs that I would like to see return in the future. Season 1 also still has some of the strongest songs, with the Gala and Art of the Dress still feeling like big budget Hollywood showtunes.
Season 3 is definitely the weakest, although part of that is due to its truncated length, there are episodes in it that I liked, with magic duel, and sleepless in Ponyville being the standouts of the season, but overall, even the midseason stuff didn't seem to be going anywhere. Season 1 had the gala and letters, season 2 had the letters, and season 4 had the journal, but season 3 didn't really have anything. The opener wasn't terrible, and some of its scenes were fun, but the songs were nothing special, and the villain was entirely forgettable.
The truth eventually came out that the season was short mostly because it was the final season in DHX's original contract, and they got the news of being picked up for season 4 after writing had already started on episodes, nowhere is this more obvious than the finale for season 3. The finale, with it's clip show and musical format, seems like it was tailormade to potentially act as a series finale, rather than just a season finale. Overall, it wasn't a terrible finale, it had some solid songs, and an interesting plot, but a major change like Twilight's coronation deserved more of a setup than what it got, at least as much as the key episodes and finale in season 4. The overall dilemma of her being made an alicorn just for fixing a spell seems kind of a letdown after earlier episodes having her help takedown major villains threatening the whole country.
In the end, Season 4 has got me interested in seeing where they take the whole castle, kingdom, spreading friendship across the land mechanic. The round table setup of the thrones is also something that could provide interesting plots in the future as the characters wrestle with potential political or social power of their own.