The problems I have with modern UI/UX design are as follows:
1. It is often tailored to the needs of mobile interfaces instead of the needs of desktop computing environments, often resulting in certain UI interactions being more complex with modern applications than with older applications that were designed for desktop users. For example, hamburger menus make sense in environments such as smartphones where room is scarce. However, I believe they are inappropriate in desktop environments, yet they are becoming more commonplace on websites (even when browsing on a desktop) and in applications. Another example is a trend in newer versions of GNOME and macOS where the title bar is fused with the toolbar. While this does save space, it makes it harder for me to rearrange windows on the desktop since I must look for empty space in the combined tool/title bar to click to drag (and sometimes not all empty space in this area drags the window), while this was never a problem for me with traditional title bars.
2. We've lost certain affordances that were present in the 1990s versions of Mac OS and Windows that aid in usability. It's harder to visually distinguish between clickable and non-clickable portions of a window in many modern applications. Scroll bars provide useful feedback while reading content that doesn't fit within the window, yet it's a common trend in modern UIs to hide the scrollbars, and when they do show up, they are often very skinny, making it harder to scroll with them (yes, trackpad gestures and scroll wheels make this less of an issue, but not everybody has nice trackpads or mice).
3. The rise of applications that refuse to adhere to platform guidelines, preferring to be "special snowflakes" for branding reasons, engagement metrics, developers' convenience, or cost reasons (it's cheaper to make an Electron app than to make separate UIs that conform to each platform's respective guidelines). The notion that applications should follow a platform's UI guidelines is increasingly fading away, and is being replaced with the attitude of, "You should be grateful that you are able to use this application." The Web, with its lack of UI guidelines and its emphasis on siloed applications instead of interoperability among applications, is taking over the desktop, with unfortunate consequences for the future of desktop computing.
There is nothing wrong with the idea of taking the substance of UIs from the 1990s and having updated color themes, icons, and fonts for them. I personally believe the pre-Yosemite Aqua interface of macOS and the Windows Vista/7 interface were great examples of modernized UIs that were desktop-tailored and retained or even enhanced affordances that were present in previous versions of these interfaces. I feel we lost a lot when the industry shifted to mobile computing and decided that desktops should look and feel more like smartphones and tablets instead of continuing to improve on the desktop computing experience.