It seems that, at this current point in time at least, that all the Panty and Stocking with Garterbelt finale was was just Gainax being…erm, Gainax. That said, with the latest evidence from the director himself, there might actually be a second season of the anime in the future, under the condition that not only the director himself feels up to it, but also if the merchandising of the franchise does well itself.
Hiroyuki Imashi, director of the anime, made a side comment during the final broadcast of Panty and Stocking, saying that a second season could be up to the sales of merchandise, including the then not-yet-released original soundtrack, as well as his own interest in the project. Another hint at the possibility was found at the end of the Panty and Stocking OST as well, which had a short segment featuring Panty and Stocking talking about a possible second season, which states yet again that it’s ultimately up to director Imashi for the future of the anime.
When it’s looked at one way, it seems like it’s obvious that the ending of Panty and Stocking, due to it’s bizarre plot twist and set-up for a second season, was just a joke on the fans; something that was truly in the spirit of the anime as well as Gainax. However, in the same sense, it’s not at all unlikely that Gainax continues Panty and Stocking in some form. As NagatoTEG stated, who says that Gainax has to follow it’s own plot and can’t just treat the current finale as a non-sequitur? However a second season may be treated, or even if there will be a second season at all is still under wraps, and only time will tell what Gainax’s true intentions are.