As for the setup for a six-movie saga, I think you're focusing too much on details at the start. If you truly wish to accomplish a cohesive six-part saga, you need to think big picture first. The details can be filled in later and will be much easier if you have the framework in place ahead of time. You'll already know what you should or shouldn't have in each act.
The main character in the PT is Anakin -- it's his story, and we're following his saga. Viewing the OT is viewing the saga of Luke. Focusing on Luke allows us to see where Luke succeeded where Anakin could not. Looking at them as one six-movie saga is fine, so long as you understand that you can use this to show the difference in their developments. As bad as the PT is at times, there are many parallels you can play off of between the OT and PT. Many times they're flip-flopped in some way, but the parallels are there nontheless.
For example, in ESB we see Luke is vulnerable to being lured to the Dark Side if he is not careful, as he acts rashly, throwing himself into action to save his friends, who are the only family he has left. Anakin does much the same in AOTC by leaving his assignment on Naboo to go save his mother on Tatooine, and then again to save Obi-Wan, the only family he has really. Both of them have scenes foreshadowing a turn to the Dark Side -- Luke's is in the tree on Dagobah, where he battles the Vader constructed by his own thoughts, where he is in the armor; Anakin slaughters an entire clan of Tusken Raiders, killing each and every last one.
The sets on Grievous's ship and the DS II throne room are very much alike. I found it somewhat symbolic that Obi-Wan and Anakin must journey downstairs to the Chancellor from the doorway in the third act of Anakin's arc, where Luke must climb the stairs, rising up against the Emperor. One shows the fall of the Jedi and one shows their rise, whether this is the intended message by Lucas or not. Anakin descends into darkness to beat Dooku. Luke, when in shadow under the stairs, gives in to the Dark Side against Vader, in a seeming parallel of events from ROTS. But Luke sees the parallel himself and realizes the error of his ways, giving him the difference needed to stay away from Emperor's clutches.
I'm a bit short on time here at the moment, but I'll post my list of parallels tomorrow. For now though, this looks like a very interesting project and I look forward to it being completed sometime.