Remember that plans are not necessarily "as is." Builders can use a reverse set of plans (sometimes called a mirror image) to better site a house. It's also possible to hire an architect or modification service to personalize a plan. Ask if reproducible prints or electronic CADD files are available for the selected plan. Either will make the alteration process quicker and easier.
One item to look for when evaluating a house plans' quality level is the number of structural sections which are shown on the plan. Highly detailed sets of plans will always cut lots of sectional views through the house to show every different roof framing situation. This might mean that 10 or 12 (or even more) sections need to be drawn for a large house plan. And even a small house plan should include 3 or 4 sections minimum. However, many home plans available today (especially plans purchased through inexpensive plan directories) cut corners in this department and only show one or two house section views. This means that the builder will have to guess at the rest of the house framing.
If you find a house plan that you love, but want to make minor changes, most companies can have their designers do that for you, at an additional fee. It is also possible to have your plans reversed, for instance, if your breakfast nook faces west but the view from the north side of your lot is more attractive, you can reverse it. Many of the sites selling house plans will allow you to see a reversed view, of houses you might want to build.
Having been in the business for more than 30 years, we have seen a large number of house plans which looked good at first glance. However, upon closer examination, many of these plans were found to be lacking large amounts of needed information. If a house plan is not easy to navigate or is not thoroughly detailed, then the builder is left to guess at the designer's intentions. This often means that he will "pad" his bid to make sure that he covers any unknown construction costs that may arise.