I watched that episode a second time now and my mind was quite active, so this is roughly what the title says: I'll write down the thoughts I had while watching the episode. Times mentioned are estimates/rounded. Enjoy/discuss!

3:00:

Ms. Harshwhinnie reprimands Rainbow Dash and asks her to show more professionalism. ... And I thought: Professionalism, hm? Like reprimanding Rainbow Dash and threatening to take away her coach role right in front of the whole school class?

5:30:

The CMC are trying to think of what's special about Ponyville. Eventually Scootaloo says: "It's a place where different kinds of ponies live together as friends."

Soooo... does that mean that other places like Manehattan or Canterlot are racist and/or practice segregation? Is it a taboo to be friends with a different type of pony elsewhere? :okiedokielokie:

Musical number:

I had to laugh at the fact that their walking is totally not in sync with the rhythm. So apparently this is not reserved for fan-made PMVs. Wouldn't have expected that.

When the Terrible Two did their psychological warfare, mocking the CMC for not having cutie marks, I looked at theirs and thought: Man! This would be such a great job for reformed Discord! What an awesome episode that would make!

10 minutes:

We see/hear, as a first in the show, audible thoughts - from Rainbow Dash. But Ms. Harshwhinnie's urge to be professional is 'still warm'. It's not like people with Alzheimer are watching. I remember wishing for this feature in other situations, in earlier episodes, where it would have made things feel a lot more natural, and then the first time they use it, it's not necessary at all in order for the scene to work properly. -_-

19 minutes:

When Rainbow Dash tells Scootaloo that she doesn't have to fly during the flag carrying segment of the Equestria Games if she can't, that this is what makes Ponyville so special, I couldn't help but think: Errrr... like ... special...olympics?