Not enough pattern space. I shouldn't have to create another character just for those extra patterns! Of course that problem didn't come from NL, but it's the only thing that TRULY annoys me.
...that and grass wear, I guess.
Not being able to control where villager's houses go
Well, technically you can with the method posted on the forum. It's time consuming though
Being told to take a break and then having someone setting up a time to come over. Come on! Which is it, take a break.. or play for another hour to meet someone at my house?!