And I rather like what you've done for a prologue. It's rough, as you said, but I like the duel as a frame.

It might be cool to (this phrase should prompt you to ignore what follows) have the Obi-Wan/Luke dialogue play over the opening logos as you did, then have it get quiet during the ALTAIAGFFA title card. Once the audience expects the opening logo and musical blast, kick in abruptly with the duel of the fates score.

You might be able to do without the "fear leads to anger" scene. I think the key beats to keep in your TPM prologue are Anakin's difficulty leaving his mother, Qui-Gon and Obi-Wan's (identities, and) relationship with each other, the idea that the Sith are out there, and some clue as to why they are fighting a lightsaber duel in the first place. You hit almost all of these on the head, so I look forward to what else you'd come up with.

Going the route of a single film would allow for more creativity than a three-film structure. Among other things, you might be able to use ROTS for the majority of the film, and make it seem as though Anakin really was an all around good guy until the latter end of the Clone Wars.

Nice idea, and good work so far! I'd love a good go-to single film as a stand-in for the prequels for a machete viewing. No offense intended to anyone, but I personally haven't cared for any of the prior attempts at crunching the prequels into a single film. But coming at it with the intent on viewing it between ESB and ROTJ make just make it work.