Build a town from scratch! Meaning, you decide:
-where the town hall is 
-where Re-Tail is
-where the plaza is
-the color of your train station roof
-the placement/shape of the river & ponds (with limitations & other requirements)
-where the rocks are (with a set minimum amount)
-your town fruit/which perfect fruit you can grow in your town
-how the beach is set up
-where the train station & train tracks are

Also, a bigger town, thus increasing the amount of villagers!
When villagers start to move in, they ask you where their houses should be! (Sort of like the camping situation: Should I move here? PLUS where should I live? Also kinda like in HHD)

Other inclusions:
-purchasable & plantable cherry blossom trees and other types of trees
-Increase the amount of PWPs allowed
-more room for designs
-PWPs suggested more often!!! I rarely get any!
-better conversations with villagers 
-ability to move the mayor’s house without resetting
-villagers stay in original clothing UNLESS you give them another shirt via mail/your pocket (I don’t think clothing should ever replace furniture in a villager’s home, but some may disagree with me on that…)
-PWPs get requested by all types of villagers. (Honestly it’s hard enough as it is to get suggested PWPs but you have to make it harder??)
-PWPs for the beach (small ones like benches, the picnic blanket, street lights, etc.)

I understand these ideas would take up more room and would obviously make the game more expensive.
I also understand that I am no video game designer and have no idea what kind of work it would take to make these happen.