You'll probably get what you pay for in either case. You should pay less for low levels of support and no real brand presence in the market. On the other hand, there is a lot of potential excitement getting involved in a startup where the answers have to be invented as you go along.
If you're comfortable being the guinea pig and assuming more risk, then the startup is something you should consider. If you're not, then don't. Remember that someone had to be the first franchisee of many of the huge systems you see in the market, so it can work. But many others who tried to be pioneers didn't survive the journey.
Jeff Elgin has almost 20 years of experience franchising, both as a franchisee and a senior franchise company executive. He's currently the CEO of FranChoice Inc., a company that provides free consulting to consumers looking for a franchise that best meets their needs.