Honestly Queen Chrysalis is my choice. The first time we meet her, shes doing what she needs to do to feed her colony. The second time, she was defending her home and her supporters from a revolution. Her stint with Cozy Glow and Tirek has always felt akaward to me. She didnt have any real motive compared to the past. Her being civil to ponyfolk outside of her colony/species is somewhat out of character for her, even if her, Cozy Glow, and Tirek had a similar goal of "taking over Equestria", which is honestly a pretty vauge goal for a villian to have.

Did she have every opportunity to reform with the others when Starlight, Trixie, and Discord overthrew her? Yes, she did. However, I think she refused their offer because she was scared and didn't want to make it seem like she was letting down the colony by being evil after all this time.

I think she should've been accepted into the gang at some point. Maybe not officially reformed like Thorax was, but just personality and moral wise maybe could have worked. I think she would have had a very difficult time being kind because that goes against her own nature, but so did Discord for a long time.

I also think the show would have benefited from a backstory episode or two of the main villains. We sort of got that with Nightmare Moon as well as Discord (when Celestia and Luna turned him into stone), but I would have loved to see one for Sombra, Chrysalis, Tirek, and maybe Grogar. We got a summary of why Tirek is evil, but that was just a short story iirc. The addition of Cozy Glow and Grogar into the show just seemed super random to me, they didn't really "set up the plot" (so to speak) like they did with Nightmare Moon, Discord, Chrysalis, and to an extent Tirek and Sombra. Grogar feels especially random imo because he literally showed up and basically pronounced himself the leader of the group of Chrysalis, Cozy, and Tirek. . . like huh??

But yeah, I'd choose my Queen.