Lack of standardization -
Codecs all over the place for audio/video.
Inconsistent ports
Controller options - gamepad used to be THE controller scheme for PCs (directinput), now we have shit like that uses the xbone driver. On the other hand, you can be like the poster above, use a gun that shoots car WHILE using a PS4 controller. Still, it is inconsistent.
Generational Gaps for upgrades - futureproofing is required to maintain the advantage of PC over the consoles. If your mofo happens to become obsolete for being able to handle the newer hardware required, then you are shit out of luck. On the flip side, my PC survived longer than any consoles or handheld I owned due to just need to fix the specific parts.
Terror of (and for) the uninitiated - consoles is just pop in, press key, you are playing game. PC, you just need that ONE bratty kid or that ONE know-it-all idiot that install a malware/virus/format one of your drives/use the CDDVD-rom as a cupholder/etc... to royally fuck up the PC.
Drivers - actually, this is both good and bad. Bad that you NEED to get it, good that it more often than now improves existing games or let your old hardware play newly release games when it couldn't before (forgot which gpu I had when Skyrim first came out, couldn't handle it, got the new driver, BAM, I'm playing it in medium setting which was still awesome considering how out of date my machine was).
Others -
Distraction - multiscreen can tank your productivity/playing when something else more interesting is happening on the other screen.
Too many options - I've a PS3-esque controller, a kbm, a joystick (air fighter style) previously a driving wheel and even a wii-mote-esy controller. This isn't an issue for me, but when you've kids over... they tend to fight for the controller with enthusiasm (pre-adult backseat drivers, argh), and when you've controllers that works from multiple source, shit happens.