Season 3 is underrated really. I think the real reason it got the flack it did was for it's short length compared to the other seasons. Which I think is stupid, because, you know what they say, quality over quantity. (I know there were also some fandom-splitting controversies I actually liked Discord becoming a good guy and Alicorn Twilight but disappointment started turning up as soon as it was announced the season was only 13 episodes long) If you split Seasons 1 & 2 into 2 13-episode seasons. I think Season 3 actually would stand on it's own against them. 10 out of 13 good episodes are accepted by the fandom, so that's good. Cause pretty much any stretch of 13 episodes in the show has their good or their more lackluster episodes.
Speaking of which the true worst stretch of 13 episodes to me is the first half of Season 1. The show wasn't secure in what it was yet. It may have had some classic episodes like Applebuck Season, Dragonshy, and Winter Wrap-Up. The other episodes though were either average that future episodes of the show looked far better in comparison or some I'd count of the below average ones (Ex: Boast Busters This episode is, at the very least, better than people say it is. Doesn't make it good, though and Look Before You Sleep I have no idea why people like this episode, or at least not hate it especially) The Ticket Master and Bridle Gossip are pretty bad, too. I'd say Griffon The Brush-Off was also bad, but it's grown on me, especially because of The Lost Treasure Of Griffonstone.