I'll chime in here as I'm currently working on an app that uses MapKit extensively. MKMapViews work in pretty much the same way as they did in iOS 5, no breaking changes.
The one thing that did break in my case was the feature of my app that opened up a walking route in the old Maps app. On iOS 5 this is done by redirecting any maps.google.com URL requests to the Maps app but of course this doesn't work with the new method. Thankfully they've replaced this with a generic API that allows you to programmatically create a routing request (no more string concatenation!) and pass it to any app which implements the required protocol for handling it, right now that's just the Maps app but I'm sure that selection will expand once iOS 6 is out.
The one thing that did break in my case was the feature of my app that opened up a walking route in the old Maps app. On iOS 5 this is done by redirecting any maps.google.com URL requests to the Maps app but of course this doesn't work with the new method. Thankfully they've replaced this with a generic API that allows you to programmatically create a routing request (no more string concatenation!) and pass it to any app which implements the required protocol for handling it, right now that's just the Maps app but I'm sure that selection will expand once iOS 6 is out.