How would I have fixed the Anakin/Padme relationship? They should still start off madly, incoherently in love, but after that I'd go in a different direction than Lucas. I would've set up Padme as an alternative to Anakin's life in the Jedi Order, and not merely an inconvenient, closeted adjunct. She would have personified Anakin's ability to leave the Jedi and adopt a normal life, and his rejection of this course of action would have highlighted his bellicose nature and also served as an implicit rejection of her. Padme would be all to aware of this, but for a while she'd stand by her man, hoping that he'd change.
Which, of course, he did--but not the way she'd hoped.
Anyhow, this sets up a possible choice for Anakin on which drama hinges, at least for the three or four people who haven't seen ESB yet. Will he ride off into the sunset with the girl, or leave her moping at home while he chases glory and military success? As the trilogy progresses--oh, yeah, let's start with the two of them as adults so we can kick the relationship off earlier--as the trilogy progresses, let's have Padme slowly turn against the Jedi and the state, blaming them (perhaps unjustly) for occupying to much of her husband's time, putting him into dangerous situations, making him obsessed with the Clone Wars. Anakin, meanwhile, begins to abandon his responsibilities towards his wife and sees himself not as a husband-father figure, but as a player on the galactic scale. He thinks he's fulfilling his duties to his government and his order, but in fact he is becoming "more machine than man," reacting to the demands of the authorities rather than those of his heart. And, of course, there are the ranks and the titles, the decorations and the legions of clonetroopers under his command. When Padme tells him that he's pregnant, he doesn't really care--he assures her she'll get the best midwife droids on Coruscant, then returns to his military work.
This slight, perhaps moreso than the "turn" in Palpatine's office, signals the end of "Ani" and the birth of Darth Vader, flunky of the state. Padme senses this, and takes measures to separate herself and her children from Anakin. He finds out, and just lets her go ... sure, they had fun together, but what is the fate of one woman with child measured against his great responsibilities to defend the Republic and serve his mentor, Chancellor Palpatine? Oh, it's an Empire now, and Palpatine is Emperor? No matter. There are still enemies to kill, no time to reminisce about a relationship that ended long ago.
In this scenario, I have abandoned most of the melodramatic plot threads that built up both around the real story and various fan interpretations. Vader does not accidentally kill his wife, they are not passionately in love until the end, Vader's refusal to let his wife go as per a murky prophetic dream does not drive him into the Sith (yecch). He simply accrues more and more power, becomes more important on a galactic scale, and forgets about her. I like this because it's much more gradual, and parallels my idea of how the fall should've been.
Umm, I think I failed to address the issues of chemistry, dialogue, and the general blecchyness of the PT relationship. Sorry. Let's just assume all those got fixed in this scenario.