Those are some pretty interesting observations. The one relating Sal and Ford Cruller (the old guy) is pretty apparent; the whole concept of a great, powerful mentor being defeated was (Is?) quite popular in cinema, but is something that clearly works well in games too -- obviously something Tim is fond of!
Although some are kind of loose, I think it does kind of show patterns in the way Schafer thinks when writing stories. They are always excellent so there must be some kind of magic going on when he's doing so.