Ass Pull: The writers were very forthright that the last four episodes of the season (drawing many seemingly insignificant plot threads together) were rewritten in response to fan whining. Though the precise mechanics of Lothor's Evil Plan do fall close to a Gambit Roulette of the highest order, the little details don't work and it's clearly a retcon. (Most of) The fans don't seem to care, making this a fine example of Author's Saving Throw.
Broken Base: The humor. While there are viewers who enjoy the season didn't take itself seriously as the two that preceded it, other viewers felt it was too jokey and the attempts at humor didn't work. This is rather ironic considering the previous ninja based Sentai series was much more comedic oriented.
Crossover Ship: While not a romantic ship (mostly), Dustin and Chip from Mystic Force are commonly written together as good friends due to their nerdy nature (as well as being the only two male Yellows in the franchise thanks to Power Rangers gender swapping Male Yellow Rangers from MMPR through Wild Force.
Actually, there's also Tideus of the Mighty Morphin' Alien Rangers, but most people don't even know he exists.
He also isn't the last Green Samurai Ranger with a Super Samurai Mode.
The proposal for Hexagon would've included a dark yellow member of the Thunder rangers, but as said proposal was scrapped, the idea wasn't used. Toei apparently thought it was a good idea, since when the Gouraigers (the sentai counterparts to the Thunder rangers) appeared in Hikonin Sentai Akibaranger, they were accompanied by a Canon Immigrant third member, TentoRaiger, whose color was, you guessed it, dark yellow.
Growing the Beard: Usually considered to either be when the Thunder Rangers joined the team or "The Samurai's Journey" three-parter.
Informed Wrongness: Dustin in "Tongue and Cheek". He does develop some Acquired Situational Narcissism, but he gets chewed out well-before then (which could explain why he would let the fame go to his head). And the one character really letting him have it is Shane, who later admits he was being jealous.
Vindicated by History: Inverted like Lost Galaxy. It was considered a fan favorite when it first aired but has lost a few ranks due to having betterreceivedseasons since. However, some fans do adore this season for various reasons (The tone, Lothor's plan, the designs, the Rangers themselves...), and many appreciate the Lighter and Softer approach after the drama heavy Wild Force.