I was actually going to start a similar thread so thanks for getting the ball rolling.
I haven't noticed any of the issues you listed. My issues are primarily GUI related.
1) in top portion of the caller ID and call log windows, the contact's image is covered up by the Tab swipe views control.
2) the spacing between the icons and the dock are messed up on the home screen
3) dock visible on the blinkfeed page
I have somewhat remedied these issues using xposed and the Sense 6 toolkit but it's still not quite right.
EDIT> This isn't a bug per say but it is very annoying. Every time I make a call through my car's bluetooth my phone now prompts me to choose an output device (handset, speakerphone, or car bluetooth). It defaults it to handset speakers so I have to select car bluetooth which is annoying because I'm trying to operate hands-free. The worst part is that it asks the question every time and doesn't remember my last preference.