The feature I'm most excited about is full-speed Nitro javascript engine outside safari. The impact for Cordova, web views and 3rd party browsers should be awesome.
I don't doubt that there is probably an explanation that makes sense, but based on what we know, the least malicious explanation is that they forgot to test WKWebView with local files, which doesn't make sense.
Honestly, with Apple sometimes I wonder. Safari had so, so many bugs when iOS7 launched that I no longer believe they spend a meaningful amount of time testing Safari before launch.