I appreciate the frustration, but some type of sidecar file (nfo, tbn, etc) it is pretty much the default way that most multimedia programs handle this problem (WMC, XBMC, others?). The "normal" structure is one movie per dirctory and then all the covers, fanart, subtitles etc are put there. I only say this because my brother was doing everything in the one directory (as I think you are) and it took him a bit to change, but I think he is happier now and it has allowed him to experiment with other software with a bit more ease.
TVShows seem to "normally" be all shows for a season in a directory, again allowing season art, etc to be placed here.
I have found having this structure and simplicity useful on occasion when trying to information from one type of program to another. If they both handle these simple xml type files, basic translation is sometimes easy.
Craig