By "host integration" I'm referring to how WPF exists completely independently of whatever preexisting frameworks exist in the host OS: WPF makes no attempt to integrate or use them, instead it re-implements them itself, which gives us applications that "don't seem quite right" because users are given the WPF version of some system feature instead of the original, canonical OS feature or service. One example is the control library: WPF's common controls (textboxes, checkboxes, etc) are all 100% re-implemented (they don't even use the visual styles API so they don't look the same). Another is the file open/save dialogs, or type (text) rendering, or child-window management, this list goes on.
The "Initialization delays" I speak to refer to the loading times for both the CLR and the WPF components. No matter what I do I can't seem to get it below 3-5 seconds for a completely cold start, which is very jarring if it's for a simple application. Imagine if Notepad.exe had these same delays.
OK, understood. Regarding the host integration, this is by design. WPF was supposed to rev faster than Windows and also with lookless controls the idea was that people would style these themselves in most cases. There weren't even UI guidelines for WPF because it wasn't meant to be constrained to look like Windows proper. You have to remember when it was being worked on, the common complaint was that everything looked the same on Windows.
Cold start is too slow. I think this is something they'll have to fix in Win8. Whatever Jupiter is will startup at CRT speeds hopefully, and not CLR/WPF speeds. The iPad startup for everything is amazingly fast. You'd think there was a 16-core CPU with 32GB of RAM in it.