My pet theory is that some of the crew, and the Wunder itself, are actually based off the Gekko State and it's crew from Eureka Seven.

Sumire, Koji, and Midori respectively mirror Talho, Ken-goh, and Gidget. Their placements on the bridge, their ship responsibilities, their physical appearances, and even there personalities line up. I basically always see Gidget when I see Midori.

The bird-like design of the Wunder is also way more similar to the Gekko-gou than any other ship in a Anno's own filmography.
Even the bridge is in the exact same location, as an almost mini-head hiding on the chin of what would be the pseudo-head of the bird.

And even though the Wunder's backstory hasn't been completely layed out yet, it is probably almost exactly the same as the Gekko-gou's.
"An experimental ship that was being made in secret by the military is stolen by defectors of said military and then said ship is used by said defectors to fight against said military."