they did something like that in the Clone Wars series ...
maybe the idea to move the underwater city and combine it with the cloning facility is the most promising ?
so the Bond plot makes Obi-Wan the Jedi Agent (hey even his investigation scenes could come handy!) we want or need ;-)
the whole water-planet/underwater city could really be at one location, meaning one ocean on "Naboo" or "Alderaan" - so the connection can be made without too much space travel, where it isn't needed.
would be cool to have a sunny look at the cloning facility, without the rain and storm ...