The boss battle theme heard in Skies of Arcadia bears a striking resemblance to the theme for first level of the 1989 Namco game Legend of Valkyrie.

There was going to be a sequel to Skies of Arcadia called Skies of Arcadia 2 for the GameCube and PS2, as confirmed by interviews with developers from the original team. The game never got beyond the planning phase, however, and it was ultimately never created.

The most common criticism for the Dreamcast version of the game was that there were too many random encounters. In the GameCube version the random encounters were scaled down to answer the problem.

A PlayStation 2 version of the game was planned to be released around the same time as the GameCube version. However, the PlayStation 2 port was dropped in order to focus on the GameCube version.

In the Japanese SEGA Dreamcast version of Skies of Arcadia, Gilder has a victory pose in which he smokes a cigar. This was taken out of the game in other releases and changed to the victory pose of his parrot perched on his shoulder.