I think that micro USB wouldnt suit so well in a 'docked' situation either. Where the connector needs to take the weight of the phone.
The lightening connector looks (I haven't seen it yet) like it could support the phone. So when it is sitting in a cradle you don't need to worry about bumping the unit and the connector breaking off inside the phone.
Apple is all about design and user experience. They probably hate the way a micro USB cable looks and it can only go in one way. Also they might want control of the peripheral market. I'm just guessing here.
The lightening connector looks (I haven't seen it yet) like it could support the phone. So when it is sitting in a cradle you don't need to worry about bumping the unit and the connector breaking off inside the phone.