I have no accurate statistics, but I believe mplayer to be the most popular media player on Linux. OTOH, gstreamer would most probably claim to be "the common way" for being endorsed by FreeDesktop and quite a bunch of distros (including Maemo in fact).

The implication that VLC is not obedient to standards is offensive. VLC receives a lot of invalid bug reports to support broken files from stupid embedded devices or random crappy FFmpeg-on-Windows front-ends. It is also well-known to be rather strict about properly formatted MPEG streams or SDP syntax for instance.

But obviously, you only care about Matroska. Matroska is a fine format, doubtlessly the best in terms of features coverage. But it is so damn complicated that it's easy for authoring software to screw it up, difficult to fully support on the read side. That said, VLC reads iMKV quite fine if you build the native libmatroska plugin. If however you rely on FFmpeg through VLC, then it sucks, so it depends on your VLC package.

As for those subtitle formats you're complaining, the biggest problem has been crappy support for upstream libraries. Lets face it, the maintenance history of libass is a mess. To make things worse, VLC did not see a proper release for 2 years between 0.8.6 and 0.9.2. Comparing with (s)mplayer is unfair if you use the bleeding edge SVN mplayer/FFmpeg version with the official VLC release. If you really want to compare properly, use bleeding edge master branches for both of them.