There are too many things to count;
1.
The town isn't named. Nothing is named other than the ponies. The lack of a name points to a lack of individuality, where everything is the same. This was further enforced by that song, especially this line:
They don't need to, since every pony is one and the same. They're all forced to be identical to the others, including hairstyle and length.
2. The Bakery Scene. Sugar Belle tries to act un-suspicious while telling the Mane 6 to meet her in the basement. That implies that the citizens know there are 'secret police' in the town. They know that they will be punished if they act different, and they're fine with it. Then they go inside the bakery, and Party favor mentions he wants to see his cutie mark, but feel guilty about it. The town has made the ponies believe fullheartedly that cutie marks are bad, so the ponies are all at war with themselves.
3. Guilting Rainbow Dash: From the song:
They make Rainbow dash super self conscious about her love of winning. Why did they target Rainbow with that? Somehow they knew that rainbow loved winning, implying that they knew about the Mane 6, and had prepared for their arrival. I heard that part of the song and honestly thought that there would be something like it for everypony.
And making ponies feel guilty about what they love just makes it easier to brainwash them.
EDIT:
4. The Villain Escaped! This was actually huge for me, as in every other opener and finale, the Villain either was banished, reformed, destroyed or otherwise defeated, but Starlight escaped, and is still free to wreak havoc over Equestria. And since she'll want vengeance on the Mane 6, i can see her doing some foolish things, such as freeing Tirek or searching out Mother Chrysalis.