I just want to clarify, the garden cottages at Boardwalk Inn are not "little", nor "small". As you said, they do have two floors. Each floor is easily at least as large as a regular room at Boardwalk Inn. The bedroom is on the upper floor along with a full bathroom that has both a soaking tub and a walk in shower, along with a vanity and two sinks. A living room is on the lower floor in addition to a very large powder room and a kitchenette which includes a fourth sink, counter space, storage space, mini fridge, microwave, and coffee accessories. Each floor has a large screen television. Each cottage has either a balcony or a patio depending on the layout. Many of the cottages also have a private fenced in garden. The maximum occupancy of 2 is for various reasons but it is not because this room type is small.
I'm taking the time to point this out because it isn't really a fair comparison to a standard size hotel room. In addition, these were very recently refurbished. The last time I looked, the photos shown when booking on Disney's website had not been updated to reflect the new decor.