Rhaenrya had her good qualities and her bad. I think chiefly among her bad qualities was an early-Stannis-like inability to let anything slide, thus the moment she actually gets into power she spends more time taking revenge than actually ruling. Hence, mass arrests and executions and torture, and people side-eyeing her because of putting Alicent in chains and poor Haelena committing suicide over the death of her children, hence completely counterproductive orders to execute her own dragonriders.
I’m sure we can chalk some of it up to propaganda, but some things are historical fact – Rhaenrya so alienated the people of King’s Landing that they rose up against her and killed her dragons, breaking the power of her House. That on its own discredits her as a politician.
But ultimately, Viserys II’s mistake was that he couldn’t make up his mind. If Rhaenrya was going to be his heir, he shouldn’t have remarried and had more children.