I like your suggestion of different versions of SotDS to fit in with whichever version of Star Wars one chooses. Maybe not for for the initial release, but its defintely something to consider in the future. I'd suggest something like this:
-The Trooperman Experience: SotDS exactly as you envisioned it.
-The Trooperman Experience - Christensen Edition: SotDS exacly as you envisioned, only with Hadyen as Anakin.
-The MagnoliaFan Experience: SotDS that ties into MagnoliaFan's Episode I, with Hayden as Anakin, foreign languages for Jar-Jar and the Nemoidians, and the Star Wars Main Theme to start the film.
-The Lucasfilm Experience: SotDS that fits into the offical saga (as well as ADM's), with Hayden as Anakin, the original voices for Jar-Jar and the Nemoidans, and that Star Wars Main Theme to start the film.
The first version is a given, and I would recommend the second be part of the initial release. The third version is really the least "essential" IMO, as it would only tie into another fan editor's work. The fourth would fit into Attack of the Clones as well as ADM's and many other less-drastic edits of Episode II, so it would probably be worth your while. Also, keep in mind every other version of the Saga has its subtitles in the black beneath the picture. I know you expressed a preference for them to be in the frame, but that would certainly set it apart from everything else out there (perhaps that should be reserved for the Trooperman Experiences).
I have no idea how much extra work this would take to accomplish, but those are my suggestions if you want an "all purpose" SotDS that can be viewed with any version of the saga.