The most complained about quest, based on most of the social media I've seen about Pirate101, is the Stupendor-X/Stormzilla quest. During the quest, your Pirate pilots Stupendor-X, a battle mech, against Stormzilla, a large lizard monster. You are given battle mech specific abilities and are tasked with defeating Stormzilla. This quest is part of the main storyline and, as such, cannot be skipped.
The problem that people seem to have is that you can't engage in direct melee combat with Stormzilla, due to it's epic abilities that will give her (she did lay eggs, seemingly) 2 or 3 hits to your 1. You have to destroy her eggs, so that they don't hatch into little stormzillas and hassle you, and then drag her through the fires you lay down via kiting. It's not tough, but it takes some getting used to.
A lot of the complaints suggest that this quest be removed altogether. I couldn't disagree more. One of the things that keeps an MMO fresh is quest variety, which admittedly is a bit lacking in Pirate101. The Stupendor-X quest is one of the few where you are tasked with doing something out of the norm. As the expansions are released, I'd like to see more of this: more variety, more risks taken, more ideas that we haven't seen in the game before . . . just anything to break up what can become monotony.
I think that the Stupendor-X questline is a good one, I don't think it's impossible, and I'd like to see KI come up with even more varied ideas on different types of quests.