Too much white space, huge margins, too little information
At least there's some attempt to combat this. For example, if you screenshot something and paste it into LibreOffice, the image is autosized from margin-to-margin. For bonus points, if it's in "web view", the autosizing is to window width.
Of course, this is a slightly old version of Libre Office, and I'm having trouble updating it on that computer. Then again, I should update that computer entirely, it's a several years old.
But still, it's universal. Being more modern won't fix that, even if the modern paradigm is to have whitespace to make touch screens more usable.
Text is indistinguishable from controls
That's more of a UI bug.
Too true. Especially when viewing some apps, such as those that show reddit comments.
Certain controls cannot be easily understood (like on/off states for check boxes or elements like tabs)
Seen this quite common. Especially ones which toggle between Red and Green. Fun for those who are red-green colourblind.
Everything presented in shades of gray or using a severely and artificially limited palette
I recall DOS being like that... 16 font colors, 8 background colors for the font and option to blink well before the HTML tag.
Often awful fonts suitable only for HiDPI devices (Windows 10 modern apps are a prime example)
Out of the list, I think that's the only one that a problem specifically with modern user interfaces.
Especially when manufacturers dump their old low-resolution systems.
Cannot be controlled by keyboard
and the ones that do require memorizing various hotkeys that really shouldn't be necessary.
Very little customizability if any
Really love to disable that backspace hotkey in Firefox (cause it conflicts with backspacing over content in a web form), cause that browser is taking its sweet time.
Still, there's plenty of UIs that aren't customizable. Only the major applications had the effort invested to make themselves customizable, and even then, there's still static patterns that can't really be customized.