WiFi is still normally lower cost in the medium term
3's Skype handsets only allow Skype to Skype calls, whereas Truphone allows calls to any telephone.
It is true that a given outbound call will often be the same marginal cost for a customer in the short term whether placed over WiFi or using bundled cellular minutes for network access via Truphone Anywhere, but that ignores the medium term opportunity of reducing the bundle size (and paying a lower monthly fee). Also, WiFi is typically much cheaper when travelling abroad. Truphone gives customers two good options, which work well together.
Truphone inbound via WiFi is useful for customers to make free Truphone to Truphone calls, for people who pay for inbound calls, and for those who don't have good cellular coverage. Truphone only makes a very small amount of revenue from inbound calls however, so giving customers more ways to save money on outbound calls is economically more significant.