If you do business in any state, you need to foreign-qualify in that state, which involves the same and sometimes even greater fees than if you just register locally as a domestic corporation/LLC.

For example, incorporating in Indiana doesn't save you from New York fees if you do transactions in New York. Transacting has different definitions state by state, and may include anything from accepting orders to having remote employees who work in that state. Most importantly, having a physical office in a state always requires you to foreign-qualify, so registering in another state doesn't really work for companies that are not fully virtual.

Speaking of virtual... does anyone follow the development of Vermont Virtual Corporations? What are the advantages, limitations, etc?