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.
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 Saban's decisions 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.
Crowning Moment of Awesome: Cam and Kiya's fight in "The Samurai's Journey, Part 2." Made even more impressive when viewers learn that Kiya is Lothor's younger self.
Vexacus viciously taking down Zurgane in "General Deception, Part 2."
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.
Tough Act to Follow: Even moreso than its predecessor, Wild Force. It was the first season Saban had no involvement with whatsoever, the first filmed in New Zealand, a lower budget and a new production crew with two former writers as the new producers.
Villain Decay: Lothor. He suffers it BEFORE the series even begins.
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.