Well when it comes to my least favourite episode it depends on which season, so i'm gonna chose 1 from each season:
Season 1: Applebuck Season
It just seem boring and predictable. Not to mention the lesson of the episode was very cliche but i will admit it did have some good moments, most notably the why wub woo scene.
Season 2: Hearth's Warming Eve
This episode was basicly like watching a christmas special, no real memorable moments either. I can't really think of any good scenes.
Season 3: (current) Wonderbolt Academy
This episode just felt rushed (seriously the episode felt shorter than it was), The story was not very interesting either. Pinkie Pie was also quite annoying in the episode too (which is saying alot seeing how she is like my second favourite pony). The ending seemed quite cliche to me.
So those are my least favourite episodes from each season, oh btw these are are my honest opinion and if you liked any episode i mention then thats ok. In fact thats more than ok, thats great!