I think one of the problems is that the various authors can't help but go bigger and better every time they write a new story. So what Lucas intends to be the most significant war in galactic history becomes a blip in a timeline of egregious and often comically unnecessary carnage and strife. Star Wars becomes no better than a long-running comic strip in which heroes and villains die and rise again at the writer's whim and engage in hundreds of battles, each new one making the rest a little bit cheaper.
As for your #1 point, I feel that Palpatine would have killed Windu and found another way to convert Anakin either directly before or directly after executing Order 66. Palpatine has a plan for everything he undertakes. He revealed himself to Anakin on purpose and expected Windu and the other Jedi masters watching the Temple to take the bait. He needed them to attack him to justify Order 66 and needed them to be dead so that the Temple could be taken. Palpatine would not have provoked the duel if there was even the slightest chance that he wouldn't win it. Anakin saving him could have been plan A while him killing the hapless Windu and finding another way to convert Anakin could have been plan B. My guess is that plan B would have involved kidnapping or wounding Padme and using some sort of trick to make it look like the Jedi were responsible so as to push Anakin into the Dark Side. Either way, I do not think that the ultimate outcome of the Windu duel was ever in question.