I've had a few thoughts on how to NOT kill off Padme AND keep the mystery of Vader's identity until EP V, AND keep the awesome funeral scene in ROTS. BUT before I lay them out here I'd just like to preface this by stating that this is NOT Ady's plan, its just a hypothetical reorganizing of scenes I've come up with. I don't know Ady's full plan for this yet....we're concentrated on ESB right now.
Ok, so, start with the Anakin VS Obi duel as usual. Obi wins, and leaves Anakin to burn. Cut the scenes of the emperor finding the torso formerly known as Anakin (perhaps leave his arrival in, but leave it ambiguous that Anakin is still alive) (or make strong suggestions that he is not...perhaps have Palpy just stand there looking dissapointed with what he sees)
Cut to a secondary plot line, shot, or scene (can you tell I don't remember the film much?)
Next you either have the birth, or the funeral.....if desired, one could skip the birth entirely...leaving even more secrecy and shock value to the later revelation that Luke & Leia are bro & sis. If the birth IS shown, then obviously cut out the death references.
Cut to more secondary stuff (this is just to allow for passage of time in the viewer's mind)
Now the funeral (and here it gets more complicated). The levitating bed with Padme's body on it would need to be reshot and re-inserted into the shots of it traveling down the walkway. Instead of Padme's body on the floating gurney, have some Jedi robes, possibly resembling Anakin's...or just a standard, more ceremonial, Jedi robe, and Anakin's lightsaber laying on top of it. Film a body double for Natalie Portman walking slowly behind the floaty body carrier thing and just overlay some appropriate Padme face...perhaps even her face from her funeral scene...tilted down, following solemly behind the robes and lightsaber of her dead lover. A tear could be animated running down her face (and this would be the last time we see her, leading very well (I think) into Leia's reference to her mother being sad). As for the lightsaber, you can either insert a shot of Obi picking it up, or leave it to the imagination because we clearly know that he does so as he later gifts it to Luke. Additionally this scene could either be left on Naboo (Anakin had no ties to his home planet after his mother died), OR could be moved to Coruscant...maybe more of a Jedi temple kind of setting or some such....
At some later point one could then show the knighting ceremony of Vader....who at this point would just be another random apprentice (as Palpy has had several already (though I would suggest removing Grievous as he's just bloody terrible....how you decide to replace Christopher Lee with a coughing CG robot is just a complete mystery to me). I don't have access to it at the moment, but I've posted the photo several times of Vader down on one knee, and Palpy force lifting Vader's helmet down onto his head. Personally I run the scene in my head with no real sound, only music...perhaps a muffled "Rise my new apprentice" line thrown into the background just to really sell the idea that this is just apprentice #whatever.
So theres the bulk of my idea. Obviously the scenes would need to be reordered in the film so that this all makes sense...but I think it would be easily achievable with little trouble...even the more difficult scenes are quite short, thereby requiring some greater work, but not much of it.