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.
Every set of custom house plans includes several items which need to be blown up and detailed for further clarification. If a set of plans does not provide additional close-up drawings (for things such as beam connections, deck railings, stairway construction, etc.), then it is not a complete set. It is very easy to cut corners during the planning process. But the end result will be higher costs for the home owner - and lots of frustration for the building contractor.
On the other hand, stock house plans are substantial past drawn designs by a skilled designer or architect ideally of a specific purpose or general use. The question is, why choose a stock plan over a custom drawn plan? It all amounts to various reasons that are discussed below.
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.