What makes season one so different from the other seasons is that the stories are very simple and really only take half the screentime in an episode. The other half is just the characters playing off each other in cute and/or funny ways.
One thing I really like about season one is how prominent the way the ponies control nature is. It's like the foundation of their whole worldview, and anything that defies that control is unnatural and frightening to them. It also provides so many romanticised fantastic situations for the characters to interact in.
This one might be just my imagination, but the way characters are animated feels more "accurate", despite a slight excess of 45-degree-angle poses.
Some other strengths of season one:
- A lack of any truly awful episodes.
- The general romanticism of the show is least eroded.
- Dragons were actually cool.
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I really have nothing bad to say about season one in itself. However; some decisions, like including creatures based on real ethnicities, made for good episodes at the time but created a poor foundation for a nine-season show (especially in these years).