Square footage and a nice layout can be more attractive to buyers than an extra bedroom and bath with an odd floorplan. Market value is really determined by what an able buyer is willing to pay.
Sometimes a 3rd bedrom really is just a den. Are they in the same building? If I knew the address and units I might be able to tell you more.
Location, location location.
When you buy a condominium, you are buying more than space. Finishes, views, amenities in the building all relate to the unit.
The financial health of the Homeowner's Association, the amount of reserves, the number of rentals in the building, the overall condition of the common areas / building all create or detract from the value of a unit, including the availability of financing for a purchaser or refinancing options of an owner.
I am sure you will see this list get longer as others weigh in.