Hal 9000 said:

I'd say if you're abandoning the titular "Episode I, II, then III," just make it one prequel film for the machete viewing order. That'd be a logical parenthetical flashback between ESB and ROTJ, given that the episodic numbering is being interfered with either way.

Good call. That would also probably put me at the 2:30-2:45 mark which I consider more acceptable for a Star Wars film than the typical 1:30 prequel edit.

I also might drop the idea of the Episode I prologue. It was a fun idea to test out but I don't think I'll be able to execute it professionally enough to make sense and feel seamless in the final edit.

However, my only concern with this approach is that the transition between between II and III will be disorienting. My current plan is to cut from Yoda's line "Begun the clone war has" to the opening battle of ROTS, with an accompanying "3 years later" graphic. I'm just hoping that new viewers wont be disoriented by the fact that the chancellor has been captured and the Jedi are trying to rescue him, since there's no crawl to explain that or who General Grievous is.