I play stock only so far. My top three grievances are:
Why does "Maneuver Mode" always change back from orbital parameters to the (completely useless) Roll/Yaw/Pitch display, every single time I switch between vessels? Incredibly annoying! Same thing with time display: why can't it remember that I want absolute time (UT) instead of mission time (MET)?
Save game sorting. Save games are alphabetically sorted rather than sorted by game time, which makes it really difficult to find the save I want (even finding the last save can be a struggle!). (Also I'd like save game slots where I can easily save over a previous save without having to type a save game name every time, while not having to rely on a single quicksave.)
Why do I constantly have to endure the long load time (AND the maneuver mode and time display resets) to go to Tracking Station to check if I have to switch craft? Why can't we have a list of vessels, sorted by "time to next event" (maneuver node, SOI switch, atmospheric entry) that I can check at a glance and use to directly switch vessel if needed?
Then there are lesser things, like why can't I save or even time accelerate with a kerbal on a ladder? Why did the Kraken blow up my command pod? Why does my surface craft/bulding creep along te ground even though it's firmly planted? Etc, etc...
The fact that user interface/experience is not important to the developers is incredibly annoying all by itself! These minor bugs/problems are known since many, many versions ago and are simply not fixed, even the easy ones (I say this as a programmer with many years of experience). Why do they ignore these issues?