Playing through the game's unlockable Expert Mode allows Fox to don a pair of sunglasses akin to his father's. Since Expert Mode is far tougher than the normal game (unlocking the mode being challenging itself), along with the heartwarming line provided by his father's ghost at the end of the game, this can suggest that Fox has become so skilled that he has truly become like his father.
Failing to destroy Spyborg in time results in it slapping Slippy away to Titania, forcing you to take a detour, and failing to protect the Great Fox results in it being rerouted to Bolse, both of which results in the bad ending. It makes sense, as Andross can easily take advantage of the delays to set up a robot double, allowing him to escape.
Why hitting all the switches and skipping the boss fight in Macbeth, while it's the easy way out, gives the better ending and access to Area 6? There are two reasons. Meta-wise, it takes skill to take down the switches and the game rewards outside the box thinking. Story-wise, if you beat the boss, you destroy the train but not the factory, so Andross still has several weapons left and is still too strong to take on. If you reroute the train, you also destroy the factory, meaning you truly take out the enemy supply and Venom is now open for a decisive counterattack.
