Okay, first of all, no one ever said that the "Master Game" if you will had to have a main on plot... For crying out loud, pokemon games have pretty much the same thing anyway:
1. Beat Elite 4
2. Catch All Pokemon
3-5 keep alternated between Battle Tower, Contets, Underground, things like that.
So a story line for the "Master Game" is possible.
As for the missing part, the GSC bit, that ain't exactly missing as it is in the works as we speak. There is a remake that will be released as DawnGold and DuskSilver.
I do however agree with your "customizable trainer" bit like PBR has featured.
Now as for the "too big a game", we never said it had to be on a handheld. For crying out loud, Nintendo has done multiple disks with a few good games. You got the Baten Kaitos games, Tales of Symphonia, there is a list of the games here:
http://en.wikipedia.org/wiki/List_of...GameCube_games so nothing is stopping them from doing it on the Wii.
Also something has confused me about what you said... You said that the "Director's Cut" of each version is slightly longer. I have to say BULL!!! RB-Y wasn't longer. GS-C wasn't longer. RS-E was the first to be longer. FR/LG don't go into the count because they were remakes of the past, something that is being done to GS right now as DG/DS