I haven't been able to read through all nine pages of comments so I don't know if this has been said already.
I don't think this will change much. It seems that Apple will continue to use Ive and his company for the overall design aesthetic of their products, with perhaps some of the minor details now falling to Ive's protegé's back in Cupertino.
The question is why Jonny Ive has chosen to leave Apple at all. Well, given his past history, my best guess is that he sees products such as the iPhone and iPad as having reached peak design. All manufacturers are basically producing whole-screen glass slabs. There isn't much left for a designer like Ive to do with them. Ive does like his side projects and I would imagine setting up his own company will allow him to take on new and exciting projects outside of Apple and the potential conflicts of interest that could occur if he stayed. At the same time, he still gets to do the bits and pieces Apple probably still need him to do.
Unexpected, yes, but I guess it makes sense.