Subtle it was not, but funny it was.
The appearance of the Flying Spaghetti Monster suggests that at least one of the show's writers is hip to the internet version of the the evolution vs. creationism "debate".
Watch a clip.
|Futurama||Thursdays 10pm / 9c|
|Preview - Evolution Under Attack|
The episode's robot evolution theme made me think of the finale of Battlestar Galactica, particularly when Bender finds "evidence" of ancient robots (a spring) at Olduvai Gorge. Yes it's silly, but the ending of BG was pretty silly too.
For a more serious SF take on human evolution, you could read Mike Resnick's "Seven Views of Olduvai Gorge" at Subterranean Press.
For factual information about evolutionary biology, I recommend:
Brian Switek's article "Ancestor or Adapiform? Darwinius and the Search for Our Early Primate Ancestors" in the most recent issue of Evolution, Education and Outreach.