Misty and Hikari. I don't like May.
But I still must say that all three girls get too much fandom attention. Because of them, characters like Cassidy, and female gymleaders barely get any attention and let's not forget the other Team Rocket/villains like Domino, Annie and Oakley. All of these girls are overshadowed by the three twerps.
Well, I can at least say that I liked Whitney's characterization in the anime more than in the games (in the games, she basically acts like a sore loser who cries if you win.), as well as Claire (because she at least gave Ash the badge as soon as he won the battle, unlike the games where she herself acts like a sore loser, thus forcing you to get the badge via other means.).
Also, I thought the anime showing Erika working part-time as a perfume shop manager AND as a group therapist explained her... ahem... "Sleepy Beauty" complex in the games pretty well. And Sabrina mentioned in the games that she trained herself and honed her abilities by bending spoons when she was a toddler, and that part was shown to be true in a flashback from her father.
I can't comment on the female Gym leaders from Hoenn in the Anime because, to be frank, I haven't even seen them (though from what I've read and heard, I'm not impressed with 3/4ths of them.), the same would have to be said with Gardenia (though I heard/read that they did capture her personality pretty well.), Fantina, or Candice.
As for villains such as Cassidy, Domino, Annie/Oakley (though in the original, they weren't really rockets.), I wouldn't have cared anyways since they are bad guys, and all the stories I've been taught is for me to hate the bad guy.
On topic, I'd choose Misty as being the best character. I can't really choose one way or another in regards to ships, though, since, to be frank Disney influenced my belief that love only happens when it's at first sight.