No prob.
The reason that happened is the company that was responsible for upholding Nintendo's wifi for the games during that time stopped hosting services. As a result the games were cut off of wifi sometime last year. It's pretty sad, but it's true.
In order to transfer Pokémon from 5th to 6th Gen, you need a Pokémon Transporter, as well as access to the Pokémon Bank, both of which are accessible through the E-Shop.