As far as the endings...the first run of playthrough #3 I got the C ending, and then the next time I somehow got both D and E in the same run. I guess just how the endings are structured.
The rest are just various failures to complete objectives or going the wrong way (for example, at the start of playthrough #2, just run off instead of going to the objective...that will trigger a joke ending).
I am about to start the secound route I have only beaten it once and then I started ME:A. Going deep into Nier again this week