The Holy Grail of a PT edit (if I may be so bold) is to support Ben's deception in EP4: "Darth Vader betrayed and murdered your father."
The immediate problem is twofold.
First, there is one person throughout the PT doing most of the betraying: Palpatine/Lord Sidious/Emperor. Second, there is a different person doing most of the killing: Anakin Skywalker.
The challenge in an edit--if you share my contention--is also twofold: First, you need to create a credible sense that there is ANOTHER figure (or force) at work in EP2 and EP3.
Second, you need to create an intentionally ambiguous suggestion for Anakin's death.
If you can pull off both of these elements, then you have the perfect device for supporting and maintaining The Big Reveal in EP5: "No. I am your father!" There is then no need to obsess about Padme or babies. Instead, you can concentrate on the normal details that are important for any good movie (e.g., the story telling, timing, cuts, effects, etc.).
The second challenge is the easy one: Just leave Anakin dying at the lava lake, which is what BrachioInGen does. The million dollar question is how to create the suggestion that "Anakin is near death because he was betrayed and then mutilated by someone named Darth Vader." Obi-wan, of all people, is actually responsible for the transformation of Anakin into the infamous Vader form, because it is Obi-wan who nearly kills Anakin. How's that for royally screwed up?
Well, of course, there is no other character that we can readily twist or manipulate in these prequels to draw attention away from Anakin. Anakin is the one with the arrogance and the attitude; Anakin is the one struggling with self-control; and Anakin is the one who lurks around in a hooded robe at night killing anything that pisses him off. There is no hiding this from the audience, because it is embedded into the plots and story lines of both EP2 and EP3.
It may be that the best--and perhaps only--candidate is Palpatine. That is, exploit the Palpatine/Emperor/Sidious element to contrive some confusion and/or suggestion that Anakin dies at the hands of someone other than Obi-wan. That other someone is revealed to be "Darth Vader" when we reach EP4, and then only in EP5 do we realize that (a) there have been two principal villains all along, and (b) Vader is in fact Anakin Skywalker, whom we believed had been betrayed and slain prior to EP4.
I am primarily thinking out loud here, so don't quote me or assume that I've solved these problems in the Prologue
