Ubuntu – Persian/Farsi videos subtitle problem

I would suggest using MPlayer. It's a really nice, feature-rich player, but often beginners have problem with the interface (CLI based by design) and the "too many possibilities" (which is also the result of being feature-rich player btw). "Raw MPlayer" (without frontends) allows you to position your subtitles with keys 'r' and 't', also you can try key 'a' to modify alignment. You can also learn about options and default keybindings by typing man mplayer within terminal. You can also visit the documentation of MPlayer at MPlayer's site: http://www.mplayerhq.hu/DOCS/HTML/en/MPlayer.html

You can also try to use many of the GUI based frontends written for MPlayer, like SMPlayer, Gnome mplayer, etc. MPlayer has its own GUI too, some people say it's not so good as some frontends though. On default install it can be launched with command 'gmplayer' or by looking the menu item showing installed softwares (make sure you haven't tried the nogui version - from the package name - because it has not got GUI support compiled in!).

About your question: mplayer can use TTF fonts, shaded/antialiased, positioned, etc as subtitles, so as far as I can imagine it should be enough for your needs, if usability is not a problem at least :)

try gnash seems to fix the flash bugs for me sudo apt-get install gnash