Action Girl: By the end of one route, your team consists of Krystal, Katt Monroe, Lucy Hare, and Amanda, who get to defend planet Corneria. It leads to a big feast prepared for the guys while they're off on Venom.
Amazon Brigade: One branch of the story results in the team of Krystal, Katt, Lucy, and Amanda, who protect their home while the usual cast is attacking the enemy homeworld. Oddly for the usual approach to Multiple Endings, this squadron never becomes official.
Ambidextrous Sprite: Well averted, where character graphics in the briefing scenes can appear from their left or their right side, but have two separate graphics for each side — not only do asymmetrical features always appear on the proper side, but the cell shading always appears to come from the same lighting angle even for characters that would otherwise appear symmetrical.
And Now for Someone Completely Different: Happens in some paths, although there is usually some relevance. The only problem is that the game doesn't bother to explain why ROB and the Great Fox are suddenly commanded by someone else.
Babies Ever After: Certain endings show the offspring of the team. Slippy and Amanda end up having at least six children (all unnamed) in one ending, while in another one Slippy's son ends up joining a possible future team composed of Fox and Krystal's son Marcus (the leader of said team), Peppy's granddaughter (presumably Lucy's daughter, father unknown), and elderly Falco.
Badass Grandpa: Peppy is still quite capable of flying an Arwing despite his age.
Bittersweet/Downer Ending: Most of Command's endings fall in between these; Ending 1 is the only ending that seems truly happy, despite hinting at Dash's Start of Darkness. Every other ending involves some combination of Star Fox disbanding, Krystal leaving, and/or a teammate depressed on missing out on the main action. The most depressing would probably be Ending 4, which shows Krystal becoming a pariah despite helping to save the universe and being rejected/shunned everywhere, until she becomes a lonely bounty hunter whom not even Fox recognizes when they cross paths years later. The accompanying ending melody aids the Tear Jerker feeling of these endings.
Canon Discontinuity: Much (possiblyall) of the game has been deemed non-Canon; at the very least, all but one of the nine different endings is non-Canon, although early Word of God suggested that the next game will likely pick up midway through Command and follow an unseen tenth ending.
Continuity Nod: The Lylat System should look familiar to anyone who's played Star Fox 64, as that is where the locations come from, though a few are missing from 64. (With Bolse and Area 6, their absence is because of the fact that they were artificial structures made to protect Andross's base, one of which was assaulted by the Star Fox team on their way to said base during the events of that game.)
Create Your Own Villain: In some endings, Dash Bowman, initially hoping to join Star Fox, turns evil in response to choices made by other characters.
A Day in the Limelight: Several of Command's branches follow characters other than Fox. Characters that benefit include Falco, Slippy, the whole of Star Wolf, and newcomer Lucy.
Fog of War: You can scribble a bit of it away with the stylus, but it grows back in after the end of a turn.
GPS Evidence: In Command, ROB is able to pinpoint Venom as the origin point of the Anglar army... because their ships are made out of a noncorroding metal, which means they can function in Venom's caustic seas. Kind of a leap of logic.
Unless you notice that, in the opening blurb, the Anglar Emperor had already declared that he and his army were from the Venom sea. Fox must not be able to get cable news aboard the Great Fox.
The Greatest Story Never Told: One of the first branches is simply "I wonder what Falco is up to?" which immediately shifts over to Falco's point of view, and continues in a linear path as Falco has his own set of adventures, leading him to a battle with Pigma. Unfortunately, this doesn't intersect with the main plot at all, which causes him much grief when he realizes he missed out on all the fun and glory.
Happily Married: Fox and Krystal in one of the endings (having one child, Marcus). Slippy and Amanda in most of the endings (having a whole lotta children). And what little we are told about Vivian, Peppy's deceased wife, suggests that they also fit the trope when she was still alive.
It's Not You, It's My Enemies: Fox's concern over Krystal's safety is what causes him to kick her off Star Fox prior to the events of the game. She doesn't take it well.
In the core team of the same game, Falco is the Fragile Speedster (low health but long boost meter) and Slippy is the Mighty Glacier (lots of health, strong weapon and several bombs, but short boost meter).
The same can be said on the Star Wolf-specific stages, with Wolf being Jack of All Stats (albeit closer to a Lightning Bruiser, since the Wolfen is basically an Arwing with vastly improved firepower), Leon is the Stone Wall (high armor but heavily reduced in firepower, he can only fire charged shots and requires lock-on), Panther is the Glass Cannon (his zapper obliterates everything but he has weak armor, not that his good boost prevents him from barrel-rolling to defend him), and Krystal is The Ken (pretty much very balanced like Fox).
Legacy Character: The game actually features three generations of the McCloud family in one. Fox is of course, a main character, but James also makes a brief appearance, and one of the endings features Marcus, the son of Fox and Krystal, leading a future Star Fox team. Said team is also made up of Slippy's son (one of many children according to another ending) and Peppy's granddaughter, with Falco seemingly taking the same role that Peppy used to as team mentor.
Story Branching: After completing the game once and receiving a relatively mundane ending, the game unlocks alternate story paths the player may select after completing each mission - these progress through different areas (with different party members), branching and interleaving to yield a total of nine distinct Multiple Endings.
Timed Mission: The game has a timer for combat in general (fuel) and a turn limit for each mission.