The aliens. Even Shima and Kouta cheered when they managed to shoot down one of the bugships; but in retrospect mankind would have been doomed had not the aliens grabbed a Foundation and thrown it into the Cosmic Fracture in front of watching humans. Only in this way could the nature of the Fracture and the cure against it be figured out before it reached the solar system. There is a subtle message in this, that you sometimes cannot discern your enemies from your saviors.
Stellvian programming: It seems like programming is entirely graphical, with code being represented as geometric figures, making use of the exception strength of human eye-hand coordination and pattern matching capabilities. Their touch-area "keyboards" still require a bit more sideways wrist movement than I would have recommended, though. Of course, speed and precision may be more important than ergonomics in such an environment.
Kissu: Mouth to mouth kissing, which has fairly recently risen to popularity worldwide from a rather obscure local custom, still seems to have the same meaning in the future. I expect fan art to belabor this point sometime.