Or maybe it's about the version of libavfilter? I'll probably wait until debian multimedia gets newer ones. Meanwhile I can use (K)MPlayer on N9 to view subtitles.

If you need a good MPlayer frontend for desktop I suggest you to try out SMPlayer. Last time I checked (few years ago) the playback quality and subtitle rendering in MPlayer were noticeably better than in VLC. VLC has nice GUI though, but SMPlayer isn't bad either. My favorite feature is automated subtitle download/upload from opensubtitles.org.

I think you told earlier about audio video sync problems when playing some files on N9 with KMPlayer using MPlayer as backend. Here is a likely remedy for that. Try autosync=30 in ~/.mplayer/config to use more agressive a/v sync. Also you can look for "mc" flag (sets maximum allowed correction in seconds) in the documentation.