When my brother built his first guitar (electric), he purchased a kit. What he found is that while the components will make an impressive beginner guitar, the electronics and other items are not the high quality that he hoped to achieve. As a result, he had to purchase a number of substitute parts in order to get there, and therefore ended up with a lot of parts that he will never use. He told me he would never buy another kit again. He does shop for unfinished guitar bodies on Ebay, then buys the other components that he needs separately.
From his experience, I would summarize by saying that you need to determine what level of quality you want to achieve. A trip to Guitar World will show you the amazing difference in quality and the cost factor. If you're looking for a beginning guitar, a kit would serve you well.