I know people like the new theme overall, however...
Our minds are incredibly powerful at differentiating between objects based on depth cues because it does it constantly when we look at real world objects. The early UI designers knew this fact and used it to great effect when UIs became more complicated.
Flat themes throw all of this out the window, and instead require us to spend more time trying to figure out what we can interact with and what is just informational, where one thing ends and another starts. Requiring mouse-overs to make controls discoverable is a bad way to make up for the loss of being able to subconsciously differentiate between UI elements.
This trend started when Microsoft brought their Metro theme from Windows Phone over to the desktop in Windows 8. Flat themes might work on a phone where the UIs are much more simple and there are no overlapping windows. So all of this is based on a phone that lost the platform wars and rumors are MS is giving up on it (I say as someone that still has a Windows Phone - so please... I'm not a hater)
That's my main complaint with Windows 10, as I have closed/moved/resized the wrong overlapping windows much more frequently now that it has become harder to tell where one thing ends and another starts. To me that isn't a step forward, it is a step back.
It doesn't really have anything to do with skeuomorphism, although being overly 3D-ish isn't a good thing either. It is possible to make beautiful modern looking UIs that still contain depth cues. I just hope the Mercury theme isn't removed at some point. And that new non-flat themes are added in the future as well.