Andrew's "Mechanical Monkey Head" Boss fights in exactly the same style as Andross, the Final Boss of the previous Star Fox Games.
The Aparoid enemies are a reference to The Borg, a mechanical race in Star Trek with a similar desire to assimilate everything.
On top of having Xevious as an unlockable extra, the Japanese version has Battle City and Star Luster unlockable as well. The latter two are still present in the western versions, but only accessible with cheat codes.
There is an unused game over theme in the game's data that resembles the game over theme from Star Fox 64 (1997).
Leon and Panther are voiced by David Scully who is best known for voicing Sergeant Johnson from the Halo series and Dimitri from Sly Cooper: Voleurs à travers le temps (2013). Like most other Star Fox: Assault (2005) voice actors, he was unable to reprise his characters' roles in Super Smash Bros. Brawl (2008).