Mane6 Chemistry

Subject: What makes the character interaction in Season 1 so special?
The way I see it, in season 1 the stories weren't big enough to fill the entire 22 minutes. This led to many "filler" scenes of the characters just talking to each other and not really advancing the plot. Because they were actually well written and were often funny while showing deeper character, these scenes seemed to be one of the big things that made the show special. Remember when they were headed to Froggy Bottom Bog and doing nothing but worrying about what might happen to Fluttershy? Or when they were all standing outside Rarity's room wondering how to make her feel better? Even with filler, I don't think anyone accused a season 1 episode of being "rushed".

Compare that to season 3. None of those precious scenes would make it in a season 3 episode, because the stories were too big even for 22 minutes. The character interaction tends to be a lot more bare-bones, if not outright forced. It's there because it needs to be, not because they have the privilege to put it there. I think it's no coincidence that people seem to prefer season 1 Pinkie humor to season 3. Her humor thrives when it doesn't really matter, and she can deliver an out-of-place line that's quirky but doesn't steal the scene. But in season 3, every spot she gets is a precious moment they have to shove in some gag for her to establish her character with. This leads to the claims of her charm being flanderized into "lolsorandomness".

Details:
Most of the stereotypes respond in a likable/acceptable manner. Each of them are like magnets, if someone says something, another two will reply to that comment, but not turn it into a full blown discussion. That is the subtlety people are talking about.
Also because they are pure/end spectrum stereotypes. Every action they do is related to their personality. e.g. Rainbow Dash crashes through the ceiling or window. Twilight tells Pinkie to keep quiet cause she's trying to concentrate, mostly on a book. Rarity tells Pinkie she refuses put the dress on her if she's all sweaty.
They never let go of their stereotyical traits.

Most of their common traits are also likable, mostly cause it's tolerable to a level. The replies will have some wit, but they won't be too offensive or demanding/ridiculouse.
ex: Dragonshy: Dash's anger is understandable, considering what a complete wuss Fluttershy is, but they don't go out of their way to kill or insult each other like Hearts Warming Eve or TheLastRoundup. Also Flutters/the writer pretty much forces everyone to interact with her cause otherwise she'd just sit there in one place, Twilight only ignores her one problem cause the writer needs to advance the plot, rather than everyone ignore every single thing she says like the typical way a shy character is handled.