That's because you chose the wrong answer when Tom Nook asked you a certain question. There are 3 answers to choose from. Obviously Nookingtons has a lot more items, so you need to choose "more selection" or something of that sort to keep Nookingtons. You choose "more hours" to get Nook n go (i think)
And I forgot what the 3rd answer is, but it gives you Nookway. (or I got Nookway and Nook n' go mixed up, but I know Nookingtons is right)