All seasons count.
I'm rewatching FiM again and here are the ones I always skip in season one:
-Feeling Pinkie Keen (Twilight learns that Pinkie has powers that make no scientific sense and she learns she has to just believe... ahem, the atheist in me really hates that one
)
-Over A Barrel (using real world colonialism to teach sharing)
Both of those were written by the same guy. I guess I don't like his work.
Then I also don't care for
-That 100th episode that is just brony fanfiction
-Simple Ways (this felt like a bitter dude wrote it)
-Horse Play (Celestia is a bad actress... just... who cares?)
-Power Ponies (SDCC tie-in I just don't care for)
-Everything in Appleoosa (I think I just hate Appleoosa and its people after Over A Barrel
)
-Too Many Pinkie Pies (my worst nightmare)
FiM episodes I love to rewatch: A Bird in the Hoof (still the most hilarious to me), Green Isn't Your Color, Amending Fences, The Mane Attraction, basically all Maud Pie and Luna episodes, A Royal Problem, Make New Friends But Keep Discord, A Canterlot Wedding, Princess Twilight Sparkle (I actually love how she became a princess and the song all princesses sing together), the ones with Thorax because he is adorable, The Road To Friendship and All Bottled Up (so relatable).
I might have missed some I love because the good outweigh the bad for me.