The problem is designers who take 'flat' as 'literally nothing indicating its interactivity.'
I personally like the current idea of "modern" UI, although it does tend to get too bloated at times. I generally prefer something minimal compared to old designs which weren't consistent, made heavy use of shadows and were pretty chaotic. Don't try to tell me old UI was playful (although as evidenced in the post, skeuomorphic UI _can_ be).
The point about some interfaces' usability being hampered by flat UI is valid. Complicated applications full of buttons with single-color icons are very hard to navigate. I find this especially true for GTK apps where the design system enforces a very specific icon style. Example: Pinta was designed to be very close to paint.net, but due to its flat design, it is very hard to navigate. On the other hand, while paint.net may look a little outdated, the design is consistent and optimized for efficient workflows.
I think the ideal design is somewhere in between flat and skeuomorphic. IMHO programs like Office and Inkscape make UI elements clear, while maintaining the ability for efficient workflows. Icons are simple, but a touch of color makes it trivial to distinguish between them.
Not every UI design is perfect for everyone, but interfaces should be designed with different needs in mind. "Power users" most likely just need better keyboard support and care less about how the UI looks.