Right now, it seems that the only control we have over what Plex selects as it's subtitle track is language based, yet in MKVs we have the option of flagging tracks as default. In most video players, the subtitles with the default flag will be selected first, but not so in Plex HT and Plex Web (unless I am mistaken).
For my uses, I would like to be able to have English subtitles for English movies (for foreign dialogue) as default, but for anime, I'd like to choose Japanese audio and full English subs by default. When there is an English dub there are two English subtitles, one for the English audio and one for the Japanese. This would be easy to do if I could just rip a blu-ray, edit the MKV, set the default flags and have Plex set to recognize this. I can't seem to find a way to do this currently with Plex, but there may be something I overlooked. My first instinct was to set defaults though, and I think it would be a good feature to let us make use of this flag.