Main street was honestly so much fun, I miss it like crazy, though I think I prefer the city that City Folk had over it. Store upgrades were great too as it gave you more to work for.
Also miss Tortimer's island. Was a lot of fun, and was very cool to have one place stuck in summer as well as the island tours and all that.
I guess for me it's the NPC interaction that honestly bugs me the most. I'm fairly new to the game, but this game seriously lacks the NPC interaction that prior games had. I really feel like it lacks soul honestly, but am still having a great time with it.
One of my biggest issues is I absolutely hate that they removed the museum descriptions for the fossils, bugs and fish when you check the displays. I think it's now you have to show Blathers and he'll tell you more about each of them. It's WAY better just to have the description on the display when you read whatever fossil, bug or fish you have on display. The museum is one of my favourite things in the game and something I love working towards to get the satisfaction of going there after collecting a bunch of creatures, art, fossils, and reading the descriptions.