The Direct-i (The miniature robot that deploys from the new Gyrowing), bears a slight resemblance to the NES accessory R.O.B.. Which makes perfect sense as the Star Fox team's Robot Buddy, R.O.B. 64 is named after said accessory.
Many people complained why all the Cornerians (and by default, General Pepper) are dogs, especially in the anime short. This become especially relevant during the final battle against Andross, when he invokes Fantastic Racism against canines on Fox and after defeating Wolf at Venom, he expresses disbelief at suffering defeat at the hands of a fox.
Players have also brought up why you can't hear any of the characters' voices unless the Wii U volume is on. Considering how the Wii U is entirely cockpit view, this was more than likely the game's version of maintaining radio silence; turning the volume up or down is essentially like cutting off radio activity inside of the plane you're flying.
Why is the Attack Carrier now a late-game boss? Because, with Andross's teleporters, it isn't needed on the front lines.
In the Area 3 mission, Pigma makes a brief quip about Fox turning him into pork chops. It's possible this was just a small joke about his species, but considering the subtle Fantastic Racism in the game, he may have been implying something else...
