different packaging systems

Erm, the fact that everyone is always talking about it and I don't have it. Maybe one day.
Alternative, the fact that Xenia is not real.

the compose key does a lot less out of the box than wincompose on windows, and the configuration is really hard to understand :c

Somehow my laptop cannot sustain more than 15 watts of tdp nor make the fans spin real loud while on Linux. Also no native Microsoft office support. If those two things weren't a problem I'd delete Windows completely.

There are a few annoyances, all interrelated, and I'd love to talk about all of them, but you said the most annoying thing, so...it's that things frequently don't work, or don't work totally correctly, and the only way to fix them is to be intimately familiar with the innards of the OS (and I don't care about some arbitrary OS to spend that much time studying it) or to do research, which can take any amount of time, and sometimes you just gotta resort to asking Linux experts for help and hoping they're nice.

i still don't fully understand what linux is

Sometimes I feel the answer is "Linux users". You don't get arguments about systemd vs sysvinit, or the GNU/Linux copypasta, or that distinct elitism from Windows users.

Apps that assume you're using a specific distro and DE (and the lack of standardization that makes them so prevalent)