The number one thing I dislike about 8.1 would be the always present battery and network indicators. I really enjoyed the fact WP didn't always show this stuff, now with the notification center swiping down to show them is actually much more useful. And what did Microsoft do? Keep them displayed permanently, without an option to disable this. Great going MS.
Next would be the redisgned photo and people hubs, now they look like apps from every average smartphone out there. I am surprised MS kept the modern or metro design within the calendar or even improved it there.