The main advantage of building a theme from the ground up is the massive educational value you get. When you develop a theme from scratch, you learn the basics of theme construction and function. This kind of knowledge will go a long way for your future projects in WordPress.
On the other hand, it's also the longest of the three paths. In a professional production environment (among people designing and developing themes as a profession), creating themes from scratch is a highly time-consuming approach, making it quite ineffective. And it's not that much about adapting the design (which must always be done with theme frameworks as well); it's more about building the core functionality of the theme.