Since upgrading vlc to version 2.0, when the subtitles are placed on a subdirectory (like ./Subtitles) vlc doesn't autodetect them. I found out that this is a bug and that it'll be fixed on vlc 2.0.2.
In the mean time I created a workaround that consists of a simple shell script that figures out the subtitles path, and then calls the vlc executable with --sub-autodetect-path parameter. Unfortunately, it only works when directly opening a file: vlc2 video_file or opening a video file via file manager. If you try to open a video file on an already running instance (e.g. Ctrl+O) it won't work, but the workaround can be used to open multiple files.
Open a terminal window and run:
wget http://goo.gl/bF6Mg -O vlc2
chmod +x vlc.desktop && chmod +x vlc2
mv vlc.desktop $HOME/.local/share/applications
mv vlc2 $HOME/bin # or replace $HOME/bin with one directory that's in your $PATH