Honestly, take away the PR blunders, bloatware, privacy nightmares, and ads, and I really just dislike how Windows works.
The file structure is the main one that really made me feel like Roddy Piper putting on the glasses. I was perfectly happy shambling around between Program Files this and LocalAppData that. As soon as I understood how logical and elegant the file structures that Linux uses is, there's no way I could ever go back.
Also, things like Settings, Device Manager, Control panel, and 2 or 3 other separate GUIs all containing A, the same settings 6 times over, or B, all containing different settings that should be consolidated. It's almost as if Microsoft can't stick with a design language or feature scope to save their lives, but they also can't get away with completely removing these old GUIs, so they just bury them and add another on top.
However, I can't say I actually hate Windows. I cut my teeth in computing on XP, and I see XPs DNA all over modern Windows (the aforementioned Control Panel being a remnant). I think without all the added garbage, Windows is actually an incredibly powerful, albiet obtuse and frustrating, piece of software.