Uh, excuse me, but what's left to defend, then?
"Greetings, my friends. We are all interested in the future, for that is where you and I are going to spend the rest of our lives."
Cinematographically, the film made sense. It effectively told its story. To be sure, the story was incredibly silly and made little sense, but the film held together well enough to tell it.
When the aliens flew to the mothership, the set where they talked to their leader didn't really look anything like the inside of a space ship, but since it was preceded by an establishing model shot, it was clear that's what it was supposed to be.
Plus, as someone else noted, the film had a certain charm to it many other films lack. Perhaps it's the fact that so much in the film was so exaggerated, much like Christopher Guest's role in Little Shop of Horrors. But more likely it's the fact that the film's humor comes across as unintentional.
A key aspect of a lot of comedy is the straight man--someone who acts totally oblivious to the humor of his situation. In Plan 9, Ed Wood is the straight man. One perceives, watching the film, that Ed Wood believes in it. When the action cuts between some nifty stock footage of artillery firing and a couple of military men talking in front of a blank wall that would be about the right shade of grey to be sky (if there weren't clouds in the real stock-footage sky) one imagines that Ed Wood probably thought the shots matched well enough that nobody would notice that they don't match perfectly (never mind that they don't really match at all).
Something like Plan 9 is hardly a good movie, but it's at least watchable. Unlike some films, I didn't find myself wondering "what was he thinking!?", since it seemed pretty clear what Ed Wood was thinking. I may have wondered "How could he possibly think ___?" [e.g. that the military studio shots matched the stock footage] but it was clear that he did. By contrast, if Manos is as described, things like the driving scenes would leave me wondering "What was he thinking!? Why is this footage here?" A much worse question.