The go-to term for the initial conflict of the Star Fox series, as told in three different installments (Star Fox on SNES, Star Fox 64, and Star Fox Zero), is the "Lylat Wars". This name originates from the original PAL release of Star Fox 64, where it was renamed to Lylat Wars due to trademark issues (similarly to why the first Star Fox was renamed to "Starwing" there as well). In comparison, its 3DS remake, Star Fox 64 3D, would retain the Star Fox 64 moniker in all regions. Nintendo would later actually canonize the "Lylat Wars" moniker as the official name of the conflict against Andross' forces in the opening prologue to Star Fox Zero.

The green planet Peppy's Arwing is shown hurdling towards in the prologue for Star Fox 64 (and also its 3DS remake, Star Fox 64 3D) is actually meant to represent Papetoon, his and also Fox and James' home planet. The Japanese prologue even refers to it as such, and various Japanese SF64 material also mention it. However, when Star Fox 64 was localized for Western audiences, Nintendo of America completely wiped out all specific mention of Papetoon in both the prologue and also manuals/guidebooks.

Star Fox 64 3D features an entirely new battle multiplayer mode unique from the battle mode found in the original Star Fox 64, where up to 4 players can play a local multiplayer match via Download Play (or alternatively, battle against CPU opponents). However, the game did not support online play.

Nintendo's Yusuke Amano explained in an interview in 2011 that the game's battle mode did not support online play due to both cost and time constraints, with the developers deciding to prioritize the 3D visuals, as the point of the project was to use Star Fox to provide users with a game that showed the capabilities of the Nintendo 3DS as quickly as possible:

The Western dub for Star Fox 64 3D notably brought back many of the original voice actors from the N64 version to reprise their respective roles for the first time in years, those being:

• Mike West (Fox, James)
• Lyssa Browne (Slippy, Katt, Spyborg)
• David Frederick White (R.O.B, Pigma, General Pepper, Attack Carrier Pilot)
• Ja Green (Leon, Shogun Pilot, Sarumarine Captain, Forever Train Conductor, Area 6 Commander)

For unknown reasons, David Frederick White goes uncredited.

The rest of the cast, however, were recasted:

• Falco, Andrew, Meteo Crusher Pilot, and Caiman, all originally voiced by Bill Johns, were now voiced by Mark Lund, Mike West, Jaz Adams and Jay Ward respectively.
• Wolf, Bill Grey and Granga, all originally voiced by Jock Blaney, were now voiced by Mike West, Jaz Adams and Mark Lund respectively.
• Peppy and Andross, both originally voiced by Rick May, were now voiced by Jaz Adams and David Frederick White respectively.