I suggest you leave the original floorplan intact. Part of your home's value is the original feel of a craftsman / arts & crafts style home - the kind of home few people have but that is often idealized. That authenticity includes the trim, wood floors, etc.
In my area, unmolested homes like yours command about a 10-20% premium over homes where the owners have made customizations such as enclosing the porch, gluing vinyl over the hardwoods, painting the stained woodwork, mixing architectural elements, putting on metal/vinyl siding, or adding ill-conceived add-ons (whatever was the trend at the moment). Plus, there are a lot more people who want a 3BR house than a 2BR house. The value hit would be huge.
More practically, it is unlikely you could seamlessly tie together the flooring and ceilings. More likely, there would need to be an ugly beam in the ceiling to support the attic joists. Also, when you remove the wall, the place where the wall used to be will be a strip where no flooring was originally installed. It is unlikely you'll be pleased with even a professional's results matching the wood grain and stain.
As lthenderson points out, if you have a cluttered bedroom and an unused bedroom, just use one of your bedrooms a huge walk-in closet and/or office and/or workout room.