These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Lord Holder Fax is something of a Magnificent Bastard as well, as he managed to gain control of seven Holds through various means, mostly conquest. One Hold, however, he "won" by marrying into the leadership...and then doing his level best to kill his Lady wife via childbirth. He also had zero problems with killing every man, woman, and child even suspected of having Ruathan blood in his bid to gain supremacy over that Hold. It's also heavily implied that he if not outright raped, then stole and coerced every half-pretty female in his jurisdiction that he could get his hands on.
Lord Holder Chalkin had a jail area that was more or less like a freezer, with small "cells" cut into rock, all of them cold and damp, into which he threw anyone that pissed him off in the slightest. A servant spilled a container of sugar and got two weeks in one of these cramped, cold cells. People were frequently kept in the cells until they died of the cold and damp, and their bodies were thrown into a lime pit, rather than given whatever passed for a normal burial. He was also heavily "tithing" his peoples' produce, whether it was food or textiles or what have you, to the point of forcing his people to starve and work themselves to death in an effort to please him while he wallowed in an excess of supplies of all kinds.
"Funny Aneurysm" Moment: In All the Weyrs of Pern, chapter 11, in a light-hearted exchange, Golanth boasts that "No feline would challenge me!", with F'lessan agreeing. Not so funny at the end of The Skies of Pern...
F'lar actually thinks to himself that he "might as well call it rape" when he has sex with Lessa and their dragons aren't involved (this is before they actually fall in love). He's vaguely troubled by this but not overwhelmed with guilt or anything, and it doesn't seem to occur to him that maybe he should stop having sex with her unless she actually wants it. He just figures he's pretty good in bed and he'll get her to come around eventually. It's not actually important that F'lar actually conceive by Lessa, and the Weyrleaders and Weyrwomen are not required to sleep with each other, so he was raping her for his own pleasure.
The way the highborn characters treat lower-ranking individuals is also pretty appalling. Lessa is bad-tempered and judgmental to the point that she nearly causes a political crisis by demanding that an insult be punished; Jaxom generally ranges from thoughtless to downright obnoxious in the way he treats commoners. Both do mature at least a bit over the course of the series.
There's also some Values Dissonance in how the disabled are treated — in MasterHarper of Pern, Robinton fathers a mentally disabled child. The child's mother urges him to go find peace and happiness by paying attention to the other boys, and not worrying about his so very disappointing retarded kid.
The drudges in general are often treated pretty badly. Given that most of them seem to be mentally disabled, this carries Unfortunate Implications.
Drudges are the equivalent of servants—most Holderfolk consider them not much different from furniture. Despicable, but not Unfortunate Implications. The reason most are mentally disabled is because no-one is a Drudge unless they have no choice—the mentally disabled can't do anything else.
Word of God on how Impression and sexual orientation work implies that riders who aren't 100% heterosexual are barred from leadership positions in the Weyr, as only heterosexuals are supposed to Impress bronze and gold dragons. (At the time McCaffrey began the series, including any roles at all for non-heterosexuals was considered progressive.)
The Woobie: Menolly. Early on, very much so. After she comes out of her shell, she's a far more assertive character that only fools would think of messing with.
Jerkass Woobie or Iron Woobie: Lessa. You really can't blame her for being so harsh and temperamental considering her family was massacred, she'd hidden as a slave in her own home for ten years, and the main reason she decided to try for Weyrwoman was because she had no clue what she'd do after getting revenge on Fax. When F'lar actually asks her about it, she realized that "she hadn't thought that far before."