Let me preface this by saying I like the phone a lot... 9 out of 10.
But since you asked about dislikes, here we go:
The damned GPS icon - this is #1 on my list, because it's the one thing I can't change. The persistent icon only shows whether GPS is on or off. There's another icon that shows when the GPS is in use, that's enough! A waste of space on the status bar that distracts from useful icons.
Power Saver Notification - this app constantly shows a toggle notification in your notifications tray with no option to disable it. I went to app info and force closed it there, but that needs to be done on reboot. Annoying and yet another thing my brain has to filter out.
Jump to the top of Blinkfeed and App Launcher - There is only 1 quick way to get to the top of those screens once you reach the bottom and I'm willing to bet most people haven't figured it out yet. Scroll down and up really quickly to get the menu bar to display, then click a new category. It's a very awkward and doesn't work consistently. I was already getting used to Blinkfeed, but I'll have to abandon it to install a 3rd party launcher.
The App Folders - it looks horrible. It turns the icons in those folders into tiny little squares that's hard to see until your eyes focus. Compare that with the stock Android folder icons and you'll want to change launchers immediately (assuming you use folders).
The Gallery - why? whyyyyyyy can't we select more than one photo at a time? why? why??? W T F. If you want to use all the features of the HTC One, such as Zoe and burst shooting mode then you MUST use the built in gallery. Just try using a 3rd party gallery and see for yourself. (I do have a suspicion as to why, but it can be fixed with some imagination).
The Alarm Status Icon - this is minor, but still bugs the hell out of me. The alarm icon is with me all day long until I disable my alarms, which puts me at risk to forget setting it back at night. There should be an option to display the alarm only X number of hours before going off. I can download another alarm app, but would be nice not to have to.
These things make me hate the phone a little bit during the day. I'll eventually get around to solving them, but I'm annoyed I have to. Coming from near stock ROM on Galaxy Nexus for reference.