I thought about placing a whole lot of information here leading up to my answer for using custom templates instead of the design wizard but I realized the Official Yahoo! Store Blog administrator summarized it best by writing the following...
That said, The Design Wizard will guide you step by step through the site design process while the Add Products Wizard will help you get your products onto your site. With just a handful of clicks, you will be able to create an attractive, professional looking, branded online store similar to the many others you may have seen.
However, for those who really want to set themselves apart from their competition and show your customers that you are really serious about doing business on-line... we have always, AND STILL DO, recommend a complete custom Yahoo! Store Design utilizing custom templates built from scratch and just for you. No "pre-built designs" or "magical wizards" will do the job for our clients and that's why we've been developing custom Yahoo! Stores for 8 years!
Don't take our word for it! Take a look at what you get and you will see that their is no comparison.