Apple made a connector that they hope might last for 10 years like the 30 pin connector. During that time, USB has gone through mini, micro a/b and now the micro USB 3 connector, and the USB forum recently announced that they are working on a new connector that should be reversible like the lightning connector. Meanwhile, Apple can choose to implement any standard they like in Lightning, just like the 30 pin connector has supported analog and digital audio, composite and component video and HDMI, all while keeping the connector backwards compatible for the main features (charging, USB and audio).
Of course there can be a benefit in making their own connector. The downsides of lack of interoperability are however way stronger and part of the intention there is clearly to prevent such interoperability, which normal user should find insulting.
