At any time during a battle when the player is selecting a command, pressing Right/Right/Left/Left/Up/Down/Up/Down/Right/Left will play a voice clip of Vyse sighing and remove his goggle for the rest of the battle. This is a purely cosmetic change and has no effect on battles.
Contributed by MehDeletingLater
Exclusive to the GameCube re-release is a set of unlockable bonus content colloquially referred to by fans as "The Three Secrets". The requirements for earning this content is as follows:
•All discoveries need to be found and reported
•The number of opened Treasure Chests must be at 90% or above
•All Crew Members must be acquired
•All Moonfish need to be captured and given to Maria's bird Piccolo
•All Wanted Battle bounties must be found, beaten, and reported
•Beat all four optional battles with Piastol and finish her story
•Defeat over 2500 enemies
•Defeat all four Sky beasts
•Win 12 non-story Ship Battles

Upon meeting this criteria, The Three Secrets can then be acquired:
1. The Mystery Merchant will now sell the Sky Fang sword to Vyse.
2. A secret discovery can be found on a peak of a rocky overpass in High Sky just outside of Sailor's Island. This discovery is a Golden Hamachou, and does not appear in the Journal after it is found.
3. At Crescent Isle, a hidden boss Spoiler:Vigoro, who in the GameCube version became an Air Pirate following his third encounter with the main characters can be fought.
Contributed by MehDeletingLater
According to the game's director and writer Shuntaro Tanaka in the Dreamcast Magazine interview published on September 10, 1999, he commented on the game's setting taking place in the skies:

"On a ship, you might scout a distant island on the horizon, but in the skies, things are hidden by clouds, and I think that makes the thrill of discovery all the more exciting. The seas have waves, but the sky has winds… we’ve prepared lots of little contrivances like that. At the beginning of the game, your map shows about 10 islands, but you’ll gradually find more—there’ll be exciting scenes where you discover whole new kingdoms beyond the clouds, lots of things like that."

"There’s all kinds of lands to discover, from huge continents to tiny islands. We want to have lots of varied terrain too, from vast sprawling deserts to smaller floating islands hidden within deep forests."

Since the game would have all kinds of varied terrain and islands, he elaborated that it would come with many different cultures to explore and discover. In particular, his team wanted to included a lot of “travelogue” elements, such as when the player heads to a new town, there would be many different shops and only local goods in that region.
Contributed by ProtoSnake
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.
Contributed by retrolinkx
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.
Contributed by MeleeWaluigi
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.
Contributed by KidDivinegon
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.
Contributed by gamemaster1991
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.
Contributed by retrolinkx