The most noticeable difference is price per square foot….but basing your decision on that metric alone is not going to tell you the whole story and if your Realtor (buyer’s agent) is telling you that the best value is the lowest square foot price, you probably should get a new buyer’s agent.
The difference in price comes from the combination of materials, selections and methods used o construct the entire home and matching your need for quality will lead you to the correct balance of price and size. It is also very important to note that the methods and materials used can have a lasting impact on the overall performance of the finishes within the home. As an example, floor joists can be spaces anywhere from 16-24 inces apart. A 16 inch spread is far more stable than a 24 inch spaced floor system and thus the day to day use by the owner will call less stress on the surrounding framing. Over time, trim will stay tighter to the drywall and the floors will tend to separate/buckle far less. Likewise, the noise transfer from room to room, nail pops and drywall cracking will also be minimal creating a far more enjoyable ownership experience.
Everyone has a budget for their new home and being financially conservative is more in vogue than it was just a few years ago. Make sure to spend as much examining the spaces between the walls as you do the finishes outside of the walls and simply buying the most size for the money is not always the wisest choice….especially if the goal is to make this your home that will be the home you plan to keep for a long time.