[[WMG:Okay, this is how the MutuallyFictional works out.]]
There are two choices, depending on which of them is the "real world".

'''Option One: ''Nadesico'' is "real", ''Gekiganger'' is fictional'''
* Okay, so we know that ''Gekiganger 3'' was made prior to Nadesico's plotline, so the only thing we need to explain here is how the Gekiganger pilots can be fans of Nadesico, which seems to be airing concurrently with the events of Gekiganger. The answer? Nagare Akatsuki is a fan of Gekiganger (or, more likely, is a former fan; that would explain his constant taunting of Akito) and used the mentions of Nadesico as the foundations for Nergal's battleship.

'''Option Two: The inverse is true'''
* ''Nadesico'' airs during the events of Gekiganger; the producers slipped in all of the references to Gekiganger as a tip of the hat to the giant robot defending Earth.

[[WMG: [[TakeAThirdOption Taking a Third Option...]]]]
The two shows are in different realities, but due to dreams[=/=]random chance[=/=][[WebComic/{{Homestuck}} author behind the fourth wall]] the other show is fictional in their universe.

[[WMG: It's possible, if you think in four dimmensions!]]
I think that after the Oddisey of the Nadesiko, the original writers of Gekikanger fell in love with those heroes, as much as as Akito and cia were in love with Gekikanger, and they made a reboot where Joe and friends are fans of Nadesiko.
Very much like Elvis was a fan of Captain Marvel Jr and inspired his wardrobe on him... and years later, Captain Marvel Jr became an Elvis fan who dressed the part!

[[WMG:Joe Umitsubame came back to life because of the existence of ''Martian Successor Nadesico''.]]
Episode 2 of ''Nadesico'' shows Akito and Gai watching Joe's death scene. But in episode 14 of Nadesico, Joe is still alive while watching episode 14. This must mean that the ''Nadesico'' writers in Gekiganger's world decided to have Joe die in the ShowWithinAShow while he was still alive in reality! The Gekiganger team must have complained to Xebec about this, so near the end of the show they decided to refer to Joe coming back to life... and through the magic of anime, it actually happened. It would be a neat reversal: in ''Nadesico'', anime causes a lot of the problems in the series, whereas in ''Gekiganger'', it saves the world.