Well, industry people will tell you that the odds of it winning when its director wasn't nominated is close to nil.
That said, there are complaints every year when female directors don't get nominated, so nothing new here.
There are always five nominations and people act like 5 is a variable number that can mean 6 or 7. As I've seen none of these movies (haven't checked the list, but unless the director of Captain America or Guardians of the Galaxy were nominated, I haven't seen the movies), I'll refrain from further debate over who did a better job.
“Driving Miss Daisy” won Best Picture and didn’t get a Best Director nomination. Rare, but it happens.