** This article has many spoilers **

Ponyo and ponyo-shaped-friends are analogy to a baby and sperms, respectively. Ponyo passes through a dark tunnel and gets into a transparent egg shaped room, which implies that a baby is carried to a mom's egg.
Not everything are exactly mapped to the process of delivering a baby but some are added to make the analogy complete and some are exaggerated.
The animation shows that Ponyo's visiting is causing a lot of troubles: the moon is falling down, ships are missing, and an entire city is submerged. This is very exaggerated but probably almost same level of troubles will be expected in a family once a baby is delivered or being delivered.

By showing ancient fish, it reminded that human species is also from sea and shares many parts on DNA. Who would easily connect dots between delivering a baby with ancient fish.
Ponyo was crossing the line between the world of magic and that of real. I thought this point of view was very romantic.
I didn't find any political factors in this animation but there was a number "1907" on a door. I am guessing that there might be some events in the year.