If Marty arrived on time to warn Doc
Near the end of part I, Marty arrived on October 26, 1985 at 1:24am, just a few minutes before Doc was shot by terrorists. He was about to drive to the Lone Pine Mall parking lot to warn Doc but the DeLorean would not start. Instead, Marty ran to the parking lot, but arrived too late. After the terrorists crashed their vehicle, Marty ran to Doc to find he was wearing a bullet proof vest and survived, since Doc had read the letter Marty wrote in 1955.
What if the DeLorean worked and Marty arrived at the parking lot before the terrorists? Let's call the Marty who had just returned from 1955 Marty A, and let's call the Marty who was in the parking lot with Doc Marty B. Since the terrorists can be seen driving past Marty A when he was unable to start the DeLorean, he would not be far ahead of them if the DeLorean had run. This means the terrorists would have shown up only a short time after Marty A. Marty would also have had to warn Doc in front of Marty B (his past self). This would have likely altered the behavior of Marty B. Doc would only have a short time to explain to Marty B that he needs to take the DeLorean back to 1955 so he can have a chance to write the letter that warned him about the terrorists. If Marty B had been killed, then Marty A would no longer exist since Marty A is a one week older version of Marty B. If Marty A no longer existed, then he could not have interfered with the events and there would be a major paradox.
It was a good thing that the DeLorean did not work, causing Marty to arrive late, since this had the outcome where both Doc and Marty survived. It is also good that Doc read the letter. Although Doc initially refused to read the letter out of fear he would disrupt the space-time continuum, if he had not refused to read it in front of Marty then Marty would not have subtracted eleven minutes from the destination time and the above paradox would have had a chance to happen. So in this cause there would have actually been less risk of distrupting the space-time continuum if Doc had initially been willing to listen to Marty's warning.
Using the neural disruptor on Biff
Near the end of part II, Biff is driving home from the dance with the almanac in his car. Doc and Marty are flying over him in the DeLorean, then they descend so Marty can chase Biff on the hoverboard. It was dangerous for Marty to hold the side of Biff's car while riding on the hoverboard. A safer option would have been for Doc and Marty to arrive at Biff's house before Biff, then once he arrived, use the neural disruptor (the same neural disruptor Doc used on Jennifer and Marty Jr. in 2015) to knock him unconscious then take the almanac. However, the hoverboard scene adds excitement, so made for a better film even thought it was not the best idea for Doc and Marty.
It also would have been necessary to wait until Biff was home from the dance to use the disruptor on him. If they had used it on him before the dance ended, it would have altered the events at the dance. With the events altered, George and Lorraine would probably not have ended up together, preventing Marty from being born.
Amending Doc's letter
On September 3, 1885, when Marty warned Doc that Buford Tannen was going to kill him in four days, they could not travel back to 1985 right away because the DeLorean's fuel line was torn which drained all the gasoline. Without gasoline, they could not bring the DeLorean up to 88 miles per hour. They came up with a plan to "borrow" a locomotive scheduled to arrive on September 7 at 8:00am to push the DeLorean up to 88 miles per hour. However, there was a simpler solution: Doc could have amended the letter he sent to Marty via Western Union asking Marty to bring a container of gasoline with him to 1885. Of course, this would have made part III a very short movie.