Skype's comments point out that US carriers all claim to be in favor of open wireless networks, while they "continue to employ various means to keep users from using devices and software applications of their choice — from terms of service to the software and firmware loaded on the handsets sold by the carriers."
They argue "An end-to-end network, in which consumer choice is empowered, ensures that innovation occurs at the edges of the network where hundreds if not thousands of application developers and software manufacturers, rather than a handful of wireless carriers, can compete to meet consumer demand."
EFF has also responded to Apple's claim that their iTunes App Store makes jailbreaking unneccessary. They gave numerous examples of software which has been rejected for the App Store, in many cases because it would compete with another product from Apple or one of their partners.
"These examples underscore the fact that there is no copyright-related rationale for preventing iPhone owners from “jailbreaking” their phones, enabling them to interoperate with applications lawfully obtained from a source of their own choosing," wrote EFF's attorneys.