1) There is no Trade mechanic. Seems odd to miss this one seeing as how they highly encourage trading with others.
2) Bugs, Fish, Seafood cannot be traded/wrapped/etc. This makes it literally impossible for some people with tight schedules to ever 100% their museums/encyclopedias without Time Travelling.
3) No Grid mechanic for public works. Isabelle is incredibly clunky and it can be hard to tell where you're even placing things. It would have been much simpler for her to lay down a town map on your desk which activates ''work mode'' where you see the town on a grid and you know exactly where everything can and cannot go, instantly.
4) Not enough to buy using medals on the island,
5) Unable to send mail to other towns.
6) No Grid mechanic for home decorating.
7) Being unable to expand or alter your town itself. New Leaf towns are very compact and it's hard to fit a lot of things very well, especially with more public works being unlocked later down the road. Villagers moving in to random locations doesn't help either as they can then completely ruin your plans/space for more public works.
8) No camera mechanic. You're zoomed in on way too much and thus have major blind spots south of you and a good chunk of your left and right views as well. It would have been nice to assign a button or two for rotating the camera, or at least a zoom in/out. I mean we have THREE running buttons. 2 of those don't need to be for running.