Getting beyond issues of plot and character, I’m left thinking about the elements of tone and style and what kind of difference the prequels would have from the original saga. I guess part of me thinks that Star Wars films can’t really work without homage of some sort, and with the original films largely doing a pastiche of sorts the old serials, one wonders what episodes 1-3 could homage to.
Truth be told, as risky as it might be, it would be interesting to have a feel in the prequels (especially in the latter two) somewhat reminiscent of the darker shades for gray films from the New Hollywood of the 70s. Create a real sense of decay in the Republic and a growing distrust of those in authority. Perhaps even throw in some film noir tropes like those seen in 40s, which has real possibilities considering much of that genre is made up of settings glamorous and clean with a seedy underbelly underneath.
Really I think, if one were careful and smart about it, making a parallel between Anakin and elements of the Republic, with the loss of idealism in both, could potentially work. Demonstrating that once the people lost faith in the Republic that it became remarkably easy for someone like Palpatine to come in and start a tyrannical reign, in and of itself is a fascinating story. The "dark times" Kenobi references could be recalling not just days of the Empire, but for the decline the led to it.
If done right, it could in a broader sense set up thematically that the events of A New Hope did for the galaxy what the Star Wars itself did to Hollywood; ushering in a bright, optimistic, era that moved passed the cynicism of the proceeding generation. It could be something that could really illustrate how the respective eras affected Luke and Anakin so differently.