Except of course the anonymity that paper tickets give. Any form of smart ticketing where the traveller's authority to pass through a gate is verified by reference to a database controlled by the issuer, can (and probably will) be used to create a continuous record the ticket's use. The justification for generating this profile will be that the issuer can better tailor the deal that you get offered by knowing how you the traveller uses its services.
A more cynical view is that a record of your rail journeys would be a useful addition to your mobile phone's locations, your face and gait recognition on street & public space CCTV, your car journeys through ANPR tracking, your credit and bank card spending etc..
Not that I am paranoid, but there's no chance of making all travel smart/electronic without a big anti-snooping furore being raised by many.