Sara decided to stay in the future, which means she will never see her parents again; they will never know where she went or what happened to her, all so that she can stay in the future to raise children she has no familial ties to.
The director specifically says he was inspired to write this anime by the Rwandan genocide and by extension, Africa and the Third World's particularly brutal dictators and civil wars. Of course, in real life, there weren't just the infamous Idi Amin or Ferdinand Marcos making hell for their people; there were plenty other brutal strongmen who didn't stand out quite as much in Western media. In other words, especially considering the environmental hardships Earth is facing in NTHT, Hamdo probably isn't the only brutal, power-hungry strongman out there.
How are Sara and Shu able to talk to each other? It's highly doubtful that Sara's fluent in Japanese and Shu in English, and for that matter what language does everyone in Hellywood speak? How are Sara and Shu able to speak to them?
Another question is why they don't use the time machine to get water.
I thought it was assumed that the time machine requires a lot of energy to use, and the limited amount of matter it can retrieve at a time wouldn't be enough to break even.
While the story only involves the conflict between Hellywood and Zari Bars, it seems logical that there are countless other settlements all over the world, located at many different altitudes, depending on where the water is. One might wonder what happens at the end of the show to all of the settlements that were located below what would become sea level. Oh those poor Ewoks.
The abortion for Sara may actually have been a non option seeing as the doctor who recommended it, and the only doctor we've seen in the series, was shot dead, and no other was mentioned.