Many people have successfully flown their own aircraft designs, and others have found design problems long after the fact. Unless you really know what you are doing, you are probably best off building from a kit, or at least a set of proven plans. There are a number of aircraft on the market that have withstood the test of time, and these are excellent places to start. Personally, I don't feel comfortable with the thought of flying around in a brand new design, or one with a very small number of examples flying. The design just hasn't had enough trial by fire.
Good designs tend to stick around, and that's also good news.
A company with good builder support that will there through the years of the product, and offer safety enhancements and modifications long after the project is flying can be an enormous asset. Building a proven design also means that you will have a better chance of finding an experienced builder when you are in the middle of your project and having difficulties. The decision to build an airplane is thus one must be made with great thought and care, but at the end of the road, when you get into your very own, brand new airplane, right out of flight testing, you'll kow whether you made the right decision. Personally, after giving it several years of thought, I have come to the conclusion that there is a homebuilt airplane in my future. Specifically, there is a Van's Aircraft RV-series airplane in my future.