!! 30bit displays are unusable under Linux. Firefox is very slow, Google Chrome is broken, KDE doesn't work, Steam crashes, etc. etc. etc.
!! High-refresh rate monitors are not properly supported as Firefox and Chrome sometimes default to 60Hz. At least Firefox has a workaround: you can set the desired refresh rate in about:config using layout.frame_rate.
!! HDR is not supported.
!! X.org has no means of providing a tear-free experience, it's only available if you're running a compositing window manager in the OpenGL mode with vsync-to-blank enabled.
!! X.org is not multithreaded. Certain applications running intensive graphical operations can easily freeze your desktop (a simple easily reproducible example: run Adobe Photoshop 7.0 under Wine, open a big enough image and apply a sophisticated filter - see your graphical session die completely until Photoshop finishes its operation).
!! Applications (or GUI toolkits) must implement their own font antialiasing
!! Very incomplete hardware sensors support, for instance, HWiNFO64 detects and shows ten hardware sensor sources on my average desktop PC and over fifty sensors, whilst lm-sensors detect and present just four sources and twenty sensors. This situation is even worse on laptops - sometimes the only readings you get from lm-sensors are cpu cores' temperatures.
!! Critical bug reports filed against the Linux kernel often get zero attention and may linger for years before being noticed and resolved. Posts to LKML oftentimes get lost if the respective developer is not attentive or is busy with his own life.
!! There's no concept of drivers in Linux aside from proprietary drivers for NVIDIA/AMD GPUs which are separate packages
!! There's no guarantee whatsoever that your system will (re)boot successfully after GRUB (bootloader) or kernel updates - sometimes even minor kernel updates break the boot proces
!! LTS distros are unusable on the desktop because they poorly support or don't support new hardware
!! Linux developers have a tendency to a) suppress news of security holes b) not notify the public when the said holes have been fixed c) miscategorize arbitrary code execution bugs as "possible denial of service"
!! Most Linux distributions do not audit included packages which means a rogue evil application or a rogue evil patch can easily make it into most distros
No stability, bugs, regressions, regressions and regressions: There's a large number of regressions (both in the kernel and in user space applications) when things which used to work break inexplicably; some of the regressions can even lead to data loss. Basically there is no quality control (QA/QC) nor regression testing in most Open Source projects (including the kernel) - Microsoft, for instance, reports that Windows 8 received 1,240,000,000 hours of testing whereas new kernel releases get, I guess, under 10,000 hours of testing - and every Linux kernel release is comparable to a new Windows version. Serious bugs which impede normal workflow can take years to be resolved. A lot of crucial hardware (e.g. GPUs, Wi-Fi cards) isn't properly supported. Often regressions are introduced in "stable" x.y.Z kernel releases even though Linux developers insist such releases must be upgraded to immidiately.
Hardware issues: Under Linux many devices and device features are still poorly supported or not supported at all. Some hardware (e.g. Broadcom Wi-Fi adapters) cannot be used unless you already have a working Internet connection. New hardware often becomes supported months after introduction. Specialized software to manage devices like printers, scanners, cameras, webcams, audio players, smartphones, etc. almost always just doesn't exist - so you won't be able to fully control your new gadgets and update firmware. Linux graphics support is a big bloody mess because kernel/X.org APIs/ABIs constantly change and NVIDIA/Broadcom/etc. companies don't want to allocate extra resources and waste their money just to keep up with an insane rate of changes in the Open Source software.
The lack of standardization, fragmentation, unwarranted & excessive variety, as well as no common direction or vision among different distros: Too many Linux distributions with incompatible and dissimilar configurations, packaging systems and incompatible libraries. Different distros employ totally different desktop environments, different graphical and console applications for configuring your computer settings. E.g. Debian-based distros oblige you to use the strictly text based `dpkg-reconfigure` utility for certain system-related maintenance tasks.
The lack of cooperation between open source developers, and internal wars: There's no central body to organize the development of different parts of the open source stack which often leads to a situation where one project introduces changes which break other projects (this problem is also reflected in "Unstable APIs/ABIs" below). Even though the Open Source movement lacks manpower, different Linux distros find enough resources to fork projects (Gentoo developers are going to develop a udev alternative; a discord in ffmpeg which led to the emergence of libav; a situation around OpenOffice/LibreOffice; a new X.org/Wayland alternative - Mir) and to use their own solutions.
A lot of rapid changes: Most Linux distros have very short upgrade/release cycles (as short as six months in some cases, or e.g. Arch which is a rolling distro, or Fedora which gets updated every six months), thus you are constantly bombarded with changes you don't expect or don't want. LTS (long term support) distros are in most cases unsuitable for the desktop user due to the policy of preserving application versions (and usually there's no officially approved way to install bleeding edge applications - please, don't remind me of PPAs and backports - these hacks are not officially supported, nor guaranteed to work). Another show-stopping problem for LTS distros is that LTS kernels often do not support new hardware.
Unstable APIs/ABIs & the lack of real compatibility: It's very difficult to use old open and closed source software in new distros (in many cases it becomes impossible due to changes in core Linux components like kernel, GCC or glibc). Almost non-existent backwards compatibility makes it incredibly difficult and costly to create closed source applications for Linux distros. Open Source software which doesn't have active developers or maintainers gets simply dropped if its dependencies cannot be satisfied because older libraries have become obsolete and they are no longer available. For this reason for instance a lot of KDE3/Qt3 applications are not available in modern Linux distros even though alternatives do not exist. Developing drivers out of the main Linux kernel tree is an excruciating and expensive chore. There's no WinSxS equivalent for Linux - thus there's no simple way to install conflicting libraries. In 2015 Debian dropped support for Linux Standard Base (LSB). Viva, incompatibility!
Software issues: Not that many native games (mostly Indies) and few native AAA games (Valve's efforts and collaboration with games developers have resulted in many recent games being released for Linux, however every year thousands of titles are still released for Windows exclusively*. More than 98% of existing and upcoming AAA titles are still unavailable in Linux). No familiar Windows software, no Microsoft Office (LibreOffice still has major troubles correctly opening Microsoft Office produced documents), no native CIFS (simple to configure and use, as well as password protected and encrypted network file sharing) equivalent, no Active Directory or its featurewise equivalent.
Money, enthusiasm, motivation and responsibility: I predicted years ago that FOSS developers would start drifting away from the platform as FOSS is no longer a playground, it requires substantial effort and time, i.e. the fun is over, developers want real money to get the really hard work done. FOSS development, which lacks financial backing, shows its fatigue and disillusionment. The FOSS platform after all requires financially motivated developers as underfunded projects start to wane and critical bugs stay open for years. One could say "Good riddance", but the problem is that oftentimes those dying projects have no alternatives or similarly-featured successors.
No polish, no consistency and no HIG adherence (even KDE developers admit it).
Various Linux components are loosely connected vs. other desktop operating systems like Windows and Mac OS X which means the same tasks running on Linux will consume quite a lot more energy (power) and as a result laptop users running Linux have a worse battery life. Here are some examples from a normal daily life: editing documents, listening to music, watching YouTube videos, or even playing games. Another example will be a simple task of desktop rendering: whereas Windows uses GPU acceleration and scheduling for many tasks related to rendering the image on the screen, Linux usually uses none.