The MU arc.
The genetically engineered folks.
Everything with Rom before they made him competent.
The FCA. The idea that the Ferengi have some central government authority that dictates how people can conduct business contradicts it otherwise being presented as a laissez-faire Ayn Rand-topia. DS9 did its best with Quark to de-cartoonify the Ferengi, but Brunt and the FCA always did their best to cartoon them back up again.