Some of the suggestions have been really good, but I think some of your ideas are making him too dark. The way I see the story of Star Wars is a story of two people, Anakin and Luke. Anakin failed miserably, and where he failed Luke succeeds and redeems Anakin at the same time. Maybe I am thinking on a totally different path than some of you, but I think Anakin needs to be a good guy, he needs to be the hero. We need him to be the guy Obi-wan talks about in A New Hope. He needs to be virtuous, to be a truly good person, but then to be drug down and corrupted. I think this was an essential point for the redemption scene in Jedi to work. I don't think it should be (but it could be) a story of the abusive father type repenting in the end of how he neglected his family (to give a loose example), but a story of dark taking over light, but light ultimately triumphing over dark in the end. I think that is the thing that will separate it from an interesting story and from becoming an epic. I don't much like the idea of Anakin going behind Padme and killing Jedi, it doesn't seem to fit. I think it would even work better, though not as dramatic I suppose, if he didn't kill his wife at all. Lets say he left her, or maybe even better yet she leaves him. This could add more to his feeling of betrayal. Perhaps he is the one involved in politics and not her, or maybe he is just a jedi who are essentially detectives/cops. Maybe he is a work aholic, coming home late every night and she feels neglected and leaves him, later it turns out she was pregnant but maybe she didn't know that when she left and never bothered to tell him, or he "died" before she got the chance. This way Vader never would have imagined the possibility of having any offspring. This could be tailored to fit the OT flawlessly (as flawless as possible that is). Imagine if after Anakin's wife leaves him she, Obi-wan, Anakin's closest friend feels she was treated badly by her husband and tries to comfort her and help her out, they could end up growing closer and closer and Anakin could discover this. This would even more rationalize Anakin's total turn from the jedi and his trying to kill his best friend. It could end with Obi-wan seeing Anakin die, but since we are viewing things from Anakin's point of view we can know that he lives. "He left me there to die, but the Sith are much more resilient than that…" I was also thinking it might be interesting to separate the emperor from the chancellor. The whole face distorting thing from the force lighting is really dumb, it might be a good way to toss it. As for when Anakin starts killing the jedi (and I think killing the kids should be dropped out all together, it is a bit too sick. At least they shouldn't be the first he kills.), imagine that some big turn happens in the movie (like when Mace dies, or something of that matter) then we have the big reveal to Anakin, after all this time of slowly being manipulated by his mentor, he now knows the jedi are a big problem, they aren't really keepers of the peace but a bunch of warmongers who won't allow the war to end. Now he is told to "go to the jedi temple and do what must be done." Anakin VO: "At that moment it hit me, I finally realized what had to be done. The Jedi Council, this whole thing was being manipulated from the inside by them, there was nothing else to be done They had to be eliminated!" It is a shame there are no scenes of Anakin fighting any Jedi, we only get to see him getting ready to commit the murder of half a dozen or so 7 years olds.
Also I was thinking if you went with Anakin's wife leaving him, you could you the scene when he enters his apartment and sits down, then asks if Obi-wan had been here. Imagine that in B&W with the VO "She left me. (sneers) She didn't even have the guts to tell me she was leaving me, I come home and find a note, then realize all her things are gone. She had really left."
Just some thoughts. I hope you get the time to make this, it is something I would really be looking forward to.